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Sample records for allen brain atlas

  1. Neuroinformatics of the Allen Mouse Brain Connectivity Atlas.

    PubMed

    Kuan, Leonard; Li, Yang; Lau, Chris; Feng, David; Bernard, Amy; Sunkin, Susan M; Zeng, Hongkui; Dang, Chinh; Hawrylycz, Michael; Ng, Lydia

    2015-02-01

    The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.

  2. Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system.

    PubMed

    Sunkin, Susan M; Ng, Lydia; Lau, Chris; Dolbeare, Tim; Gilbert, Terri L; Thompson, Carol L; Hawrylycz, Michael; Dang, Chinh

    2013-01-01

    The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate. Here, we review the resources available at the Allen Brain Atlas, describing each product and data type [such as in situ hybridization (ISH) and supporting histology, microarray, RNA sequencing, reference atlases, projection mapping and magnetic resonance imaging]. In addition, standardized and unique features in the web applications are described that enable users to search and mine the various data sets. Features include both simple and sophisticated methods for gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of ISH, microarray and RNA sequencing data, Brain Explorer software for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer. In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal.

  3. Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool.

    PubMed

    Zaldivar, Andrew; Krichmar, Jeffrey L

    2014-01-01

    The Allen Brain Atlas-Driven Visualizations (ABADV) is a publicly accessible web-based tool created to retrieve and visualize expression energy data from the Allen Brain Atlas (ABA) across multiple genes and brain structures. Though the ABA offers their own search engine and software for researchers to view their growing collection of online public data sets, including extensive gene expression and neuroanatomical data from human and mouse brain, many of their tools limit the amount of genes and brain structures researchers can view at once. To complement their work, ABADV generates multiple pie charts, bar charts and heat maps of expression energy values for any given set of genes and brain structures. Such a suite of free and easy-to-understand visualizations allows for easy comparison of gene expression across multiple brain areas. In addition, each visualization links back to the ABA so researchers may view a summary of the experimental detail. ABADV is currently supported on modern web browsers and is compatible with expression energy data from the Allen Mouse Brain Atlas in situ hybridization data. By creating this web application, researchers can immediately obtain and survey numerous amounts of expression energy data from the ABA, which they can then use to supplement their work or perform meta-analysis. In the future, we hope to enable ABADV across multiple data resources.

  4. Automatic registration of imaging mass spectrometry data to the Allen Brain Atlas transcriptome

    NASA Astrophysics Data System (ADS)

    Abdelmoula, Walid M.; Carreira, Ricardo J.; Shyti, Reinald; Balluff, Benjamin; Tolner, Else; van den Maagdenberg, Arn M. J. M.; Lelieveldt, B. P. F.; McDonnell, Liam; Dijkstra, Jouke

    2014-03-01

    Imaging Mass Spectrometry (IMS) is an emerging molecular imaging technology that provides spatially resolved information on biomolecular structures; each image pixel effectively represents a molecular mass spectrum. By combining the histological images and IMS-images, neuroanatomical structures can be distinguished based on their biomolecular features as opposed to morphological features. The combination of IMS data with spatially resolved gene expression maps of the mouse brain, as provided by the Allen Mouse Brain atlas, would enable comparative studies of spatial metabolic and gene expression patterns in life-sciences research and biomarker discovery. As such, it would be highly desirable to spatially register IMS slices to the Allen Brain Atlas (ABA). In this paper, we propose a multi-step automatic registration pipeline to register ABA histology to IMS- images. Key novelty of the method is the selection of the best reference section from the ABA, based on pre-processed histology sections. First, we extracted a hippocampus-specific geometrical feature from the given experimental histological section to initially localize it among the ABA sections. Then, feature-based linear registration is applied to the initially localized section and its two neighbors in the ABA to select the most similar reference section. A non-rigid registration yields a one-to-one mapping of the experimental IMS slice to the ABA. The pipeline was applied on 6 coronal sections from two mouse brains, showing high anatomical correspondence, demonstrating the feasibility of complementing biomolecule distributions from individual mice with the genome-wide ABA transcriptome.

  5. A Self-Study Tutorial using the Allen Brain Explorer and Brain Atlas to Teach Concepts of Mammalian Neuroanatomy and Brain Function.

    PubMed

    Jenks, Bruce G

    2009-01-01

    The Allen Brain Atlas is a repository of neuroanatomical data concerning the mouse brain. The core of the database is a Nissl-stained reference atlas of the brain accompanied by in situ hybridization data for essentially the entire mouse genome. This database is freely available at the Allen Institute for Brain Science website, as is an innovative tool to explore the database, the Brain Explorer. This tool is downloaded and installed on your own computer. I have developed a self-study tutorial, "Explorations with the Allen Brain Explorer", which uses the Brain Explorer and the Brain Atlas to teach fundamentals of mammalian neuroanatomy and brain function. In this tutorial background information and step-by-step exercises on the use of the Brain Explorer are given using PowerPoint as a platform. To do the tutorial both the PowerPoint and the Brain Explorer are opened on the computer and the students switch from one program to the other as they go, in a step-wise fashion, through the various exercises. There are two main groups of exercises, titled "The Basics" and "Explorations", with both groups accessed from a PowerPoint "Start Menu" by clicking on dynamic links to the appropriate exercises. Most exercises have a number of dynamic links to PowerPoint slides where background information for the exercises is given or the neuroanatomical data collected from the Brain Atlas is discussed.

  6. Computational neuroanatomy: mapping cell-type densities in the mouse brain, simulations from the Allen Brain Atlas

    NASA Astrophysics Data System (ADS)

    Grange, Pascal

    2015-09-01

    The Allen Brain Atlas of the adult mouse (ABA) consists of digitized expression profiles of thousands of genes in the mouse brain, co-registered to a common three-dimensional template (the Allen Reference Atlas).This brain-wide, genome-wide data set has triggered a renaissance in neuroanatomy. Its voxelized version (with cubic voxels of side 200 microns) is available for desktop computation in MATLAB. On the other hand, brain cells exhibit a great phenotypic diversity (in terms of size, shape and electrophysiological activity), which has inspired the names of some well-studied cell types, such as granule cells and medium spiny neurons. However, no exhaustive taxonomy of brain cell is available. A genetic classification of brain cells is being undertaken, and some cell types have been chraracterized by their transcriptome profiles. However, given a cell type characterized by its transcriptome, it is not clear where else in the brain similar cells can be found. The ABA can been used to solve this region-specificity problem in a data-driven way: rewriting the brain-wide expression profiles of all genes in the atlas as a sum of cell-type-specific transcriptome profiles is equivalent to solving a quadratic optimization problem at each voxel in the brain. However, the estimated brain-wide densities of 64 cell types published recently were based on one series of co-registered coronal in situ hybridization (ISH) images per gene, whereas the online ABA contains several image series per gene, including sagittal ones. In the presented work, we simulate the variability of cell-type densities in a Monte Carlo way by repeatedly drawing a random image series for each gene and solving the optimization problem. This yields error bars on the region-specificity of cell types.

  7. Analysis of chaperone mRNA expression in the adult mouse brain by meta analysis of the Allen Brain Atlas.

    PubMed

    Tebbenkamp, Andrew T N; Borchelt, David R

    2010-10-28

    The pathology of many neurodegenerative diseases is characterized by the accumulation of misfolded and aggregated proteins in various cell types and regional substructures throughout the central and peripheral nervous systems. The accumulation of these aggregated proteins signals dysfunction of cellular protein homeostatic mechanisms such as the ubiquitin/proteasome system, autophagy, and the chaperone network. Although there are several published studies in which transcriptional profiling has been used to examine gene expression in various tissues, including tissues of neurodegenerative disease models, there has not been a report that focuses exclusively on expression of the chaperone network. In the present study, we used the Allen Brain Atlas online database to analyze chaperone expression levels. This database utilizes a quantitative in situ hybridization approach and provides data on 270 chaperone genes within many substructures of the adult mouse brain. We determined that 256 of these chaperone genes are expressed at some level. Surprisingly, relatively few genes, only 30, showed significant variations in levels of mRNA across different substructures of the brain. The greatest degree of variability was exhibited by genes of the DnaJ co-chaperone, Tetratricopeptide repeat, and the HSPH families. Our analysis provides a valuable resource towards determining how variations in chaperone gene expression may modulate the vulnerability of specific neuronal populations of mammalian brain.

  8. Precise Anatomic Localization of Accumulated Lipids in Mfp2 Deficient Murine Brains Through Automated Registration of SIMS Images to the Allen Brain Atlas

    NASA Astrophysics Data System (ADS)

    Škrášková, Karolina; Khmelinskii, Artem; Abdelmoula, Walid M.; De Munter, Stephanie; Baes, Myriam; McDonnell, Liam; Dijkstra, Jouke; Heeren, Ron M. A.

    2015-06-01

    Mass spectrometry imaging (MSI) is a powerful tool for the molecular characterization of specific tissue regions. Histochemical staining provides anatomic information complementary to MSI data. The combination of both modalities has been proven to be beneficial. However, direct comparison of histology based and mass spectrometry-based molecular images can become problematic because of potential tissue damages or changes caused by different sample preparation. Curated atlases such as the Allen Brain Atlas (ABA) offer a collection of highly detailed and standardized anatomic information. Direct comparison of MSI brain data to the ABA allows for conclusions to be drawn on precise anatomic localization of the molecular signal. Here we applied secondary ion mass spectrometry imaging at high spatial resolution to study brains of knock-out mouse models with impaired peroxisomal β-oxidation. Murine models were lacking D-multifunctional protein (MFP2), which is involved in degradation of very long chain fatty acids. SIMS imaging revealed deposits of fatty acids within distinct brain regions. Manual comparison of the MSI data with the histologic stains did not allow for an unequivocal anatomic identification of the fatty acids rich regions. We further employed an automated pipeline for co-registration of the SIMS data to the ABA. The registration enabled precise anatomic annotation of the brain structures with the revealed lipid deposits. The precise anatomic localization allowed for a deeper insight into the pathology of Mfp2 deficient mouse models.

  9. Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas.

    PubMed

    Eising, Else; Huisman, Sjoerd M H; Mahfouz, Ahmed; Vijfhuizen, Lisanne S; Anttila, Verneri; Winsvold, Bendik S; Kurth, Tobias; Ikram, M Arfan; Freilinger, Tobias; Kaprio, Jaakko; Boomsma, Dorret I; van Duijn, Cornelia M; Järvelin, Marjo-Riitta R; Zwart, John-Anker; Quaye, Lydia; Strachan, David P; Kubisch, Christian; Dichgans, Martin; Davey Smith, George; Stefansson, Kari; Palotie, Aarno; Chasman, Daniel I; Ferrari, Michel D; Terwindt, Gisela M; de Vries, Boukje; Nyholt, Dale R; Lelieveldt, Boudewijn P F; van den Maagdenberg, Arn M J M; Reinders, Marcel J T

    2016-04-01

    Migraine is a common disabling neurovascular brain disorder typically characterised by attacks of severe headache and associated with autonomic and neurological symptoms. Migraine is caused by an interplay of genetic and environmental factors. Genome-wide association studies (GWAS) have identified over a dozen genetic loci associated with migraine. Here, we integrated migraine GWAS data with high-resolution spatial gene expression data of normal adult brains from the Allen Human Brain Atlas to identify specific brain regions and molecular pathways that are possibly involved in migraine pathophysiology. To this end, we used two complementary methods. In GWAS data from 23,285 migraine cases and 95,425 controls, we first studied modules of co-expressed genes that were calculated based on human brain expression data for enrichment of genes that showed association with migraine. Enrichment of a migraine GWAS signal was found for five modules that suggest involvement in migraine pathophysiology of: (i) neurotransmission, protein catabolism and mitochondria in the cortex; (ii) transcription regulation in the cortex and cerebellum; and (iii) oligodendrocytes and mitochondria in subcortical areas. Second, we used the high-confidence genes from the migraine GWAS as a basis to construct local migraine-related co-expression gene networks. Signatures of all brain regions and pathways that were prominent in the first method also surfaced in the second method, thus providing support that these brain regions and pathways are indeed involved in migraine pathophysiology. PMID:26899160

  10. Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas.

    PubMed

    Eising, Else; Huisman, Sjoerd M H; Mahfouz, Ahmed; Vijfhuizen, Lisanne S; Anttila, Verneri; Winsvold, Bendik S; Kurth, Tobias; Ikram, M Arfan; Freilinger, Tobias; Kaprio, Jaakko; Boomsma, Dorret I; van Duijn, Cornelia M; Järvelin, Marjo-Riitta R; Zwart, John-Anker; Quaye, Lydia; Strachan, David P; Kubisch, Christian; Dichgans, Martin; Davey Smith, George; Stefansson, Kari; Palotie, Aarno; Chasman, Daniel I; Ferrari, Michel D; Terwindt, Gisela M; de Vries, Boukje; Nyholt, Dale R; Lelieveldt, Boudewijn P F; van den Maagdenberg, Arn M J M; Reinders, Marcel J T

    2016-04-01

    Migraine is a common disabling neurovascular brain disorder typically characterised by attacks of severe headache and associated with autonomic and neurological symptoms. Migraine is caused by an interplay of genetic and environmental factors. Genome-wide association studies (GWAS) have identified over a dozen genetic loci associated with migraine. Here, we integrated migraine GWAS data with high-resolution spatial gene expression data of normal adult brains from the Allen Human Brain Atlas to identify specific brain regions and molecular pathways that are possibly involved in migraine pathophysiology. To this end, we used two complementary methods. In GWAS data from 23,285 migraine cases and 95,425 controls, we first studied modules of co-expressed genes that were calculated based on human brain expression data for enrichment of genes that showed association with migraine. Enrichment of a migraine GWAS signal was found for five modules that suggest involvement in migraine pathophysiology of: (i) neurotransmission, protein catabolism and mitochondria in the cortex; (ii) transcription regulation in the cortex and cerebellum; and (iii) oligodendrocytes and mitochondria in subcortical areas. Second, we used the high-confidence genes from the migraine GWAS as a basis to construct local migraine-related co-expression gene networks. Signatures of all brain regions and pathways that were prominent in the first method also surfaced in the second method, thus providing support that these brain regions and pathways are indeed involved in migraine pathophysiology.

  11. MENGA: A New Comprehensive Tool for the Integration of Neuroimaging Data and the Allen Human Brain Transcriptome Atlas

    PubMed Central

    Rizzo, Gaia; Veronese, Mattia; Expert, Paul; Turkheimer, Federico E.; Bertoldo, Alessandra

    2016-01-01

    Introduction Brain-wide mRNA mappings offer a great potential for neuroscience research as they can provide information about system proteomics. In a previous work we have correlated mRNA maps with the binding patterns of radioligands targeting specific molecular systems and imaged with positron emission tomography (PET) in unrelated control groups. This approach is potentially applicable to any imaging modality as long as an efficient procedure of imaging-genomic matching is provided. In the original work we considered mRNA brain maps of the whole human genome derived from the Allen human brain database (ABA) and we performed the analysis with a specific region-based segmentation with a resolution that was limited by the PET data parcellation. There we identified the need for a platform for imaging-genomic integration that should be usable with any imaging modalities and fully exploit the high resolution mapping of ABA dataset. Aim In this work we present MENGA (Multimodal Environment for Neuroimaging and Genomic Analysis), a software platform that allows the investigation of the correlation patterns between neuroimaging data of any sort (both functional and structural) with mRNA gene expression profiles derived from the ABA database at high resolution. Results We applied MENGA to six different imaging datasets from three modalities (PET, single photon emission tomography and magnetic resonance imaging) targeting the dopamine and serotonin receptor systems and the myelin molecular structure. We further investigated imaging-genomic correlations in the case of mismatch between selected proteins and imaging targets. PMID:26882227

  12. Brain templates and atlases.

    PubMed

    Evans, Alan C; Janke, Andrew L; Collins, D Louis; Baillet, Sylvain

    2012-08-15

    The core concept within the field of brain mapping is the use of a standardized, or "stereotaxic", 3D coordinate frame for data analysis and reporting of findings from neuroimaging experiments. This simple construct allows brain researchers to combine data from many subjects such that group-averaged signals, be they structural or functional, can be detected above the background noise that would swamp subtle signals from any single subject. Where the signal is robust enough to be detected in individuals, it allows for the exploration of inter-individual variance in the location of that signal. From a larger perspective, it provides a powerful medium for comparison and/or combination of brain mapping findings from different imaging modalities and laboratories around the world. Finally, it provides a framework for the creation of large-scale neuroimaging databases or "atlases" that capture the population mean and variance in anatomical or physiological metrics as a function of age or disease. However, while the above benefits are not in question at first order, there are a number of conceptual and practical challenges that introduce second-order incompatibilities among experimental data. Stereotaxic mapping requires two basic components: (i) the specification of the 3D stereotaxic coordinate space, and (ii) a mapping function that transforms a 3D brain image from "native" space, i.e. the coordinate frame of the scanner at data acquisition, to that stereotaxic space. The first component is usually expressed by the choice of a representative 3D MR image that serves as target "template" or atlas. The native image is re-sampled from native to stereotaxic space under the mapping function that may have few or many degrees of freedom, depending upon the experimental design. The optimal choice of atlas template and mapping function depend upon considerations of age, gender, hemispheric asymmetry, anatomical correspondence, spatial normalization methodology and disease

  13. Brain templates and atlases.

    PubMed

    Evans, Alan C; Janke, Andrew L; Collins, D Louis; Baillet, Sylvain

    2012-08-15

    The core concept within the field of brain mapping is the use of a standardized, or "stereotaxic", 3D coordinate frame for data analysis and reporting of findings from neuroimaging experiments. This simple construct allows brain researchers to combine data from many subjects such that group-averaged signals, be they structural or functional, can be detected above the background noise that would swamp subtle signals from any single subject. Where the signal is robust enough to be detected in individuals, it allows for the exploration of inter-individual variance in the location of that signal. From a larger perspective, it provides a powerful medium for comparison and/or combination of brain mapping findings from different imaging modalities and laboratories around the world. Finally, it provides a framework for the creation of large-scale neuroimaging databases or "atlases" that capture the population mean and variance in anatomical or physiological metrics as a function of age or disease. However, while the above benefits are not in question at first order, there are a number of conceptual and practical challenges that introduce second-order incompatibilities among experimental data. Stereotaxic mapping requires two basic components: (i) the specification of the 3D stereotaxic coordinate space, and (ii) a mapping function that transforms a 3D brain image from "native" space, i.e. the coordinate frame of the scanner at data acquisition, to that stereotaxic space. The first component is usually expressed by the choice of a representative 3D MR image that serves as target "template" or atlas. The native image is re-sampled from native to stereotaxic space under the mapping function that may have few or many degrees of freedom, depending upon the experimental design. The optimal choice of atlas template and mapping function depend upon considerations of age, gender, hemispheric asymmetry, anatomical correspondence, spatial normalization methodology and disease

  14. High-resolution gene expression atlases for adult and developing mouse brain and spinal cord.

    PubMed

    Henry, Alex M; Hohmann, John G

    2012-10-01

    Knowledge of the structure, genetics, circuits, and physiological properties of the mammalian brain in both normal and pathological states is ever increasing as research labs worldwide probe the various aspects of brain function. Until recently, however, comprehensive cataloging of gene expression across the central nervous system has been lacking. The Allen Institute for Brain Science, as part of its mission to propel neuroscience research, has completed several large gene-mapping projects in mouse, nonhuman primate, and human brain, producing informative online public resources and tools. Here we present the Allen Mouse Brain Atlas, covering ~20,000 genes throughout the adult mouse brain; the Allen Developing Mouse Brain Atlas, detailing expression of approximately 2,000 important developmental genes across seven embryonic and postnatal stages of brain growth; and the Allen Spinal Cord Atlas, revealing expression for ~20,000 genes in the adult and neonatal mouse spinal cords. Integrated data-mining tools, including reference atlases, informatics analyses, and 3-D viewers, are described. For these massive-scale projects, high-throughput industrial techniques were developed to standardize and reliably repeat experimental goals. To verify consistency and accuracy, a detailed analysis of the 1,000 most viewed genes for the adult mouse brain (according to website page views) was performed by comparing our data with peer-reviewed literature and other databases. We show that our data are highly consistent with independent sources and provide a comprehensive compendium of information and tools used by thousands of researchers each month. All data and tools are freely available via the Allen Brain Atlas portal (www.brain-map.org).

  15. High-resolution gene expression atlases for adult and developing mouse brain and spinal cord.

    PubMed

    Henry, Alex M; Hohmann, John G

    2012-10-01

    Knowledge of the structure, genetics, circuits, and physiological properties of the mammalian brain in both normal and pathological states is ever increasing as research labs worldwide probe the various aspects of brain function. Until recently, however, comprehensive cataloging of gene expression across the central nervous system has been lacking. The Allen Institute for Brain Science, as part of its mission to propel neuroscience research, has completed several large gene-mapping projects in mouse, nonhuman primate, and human brain, producing informative online public resources and tools. Here we present the Allen Mouse Brain Atlas, covering ~20,000 genes throughout the adult mouse brain; the Allen Developing Mouse Brain Atlas, detailing expression of approximately 2,000 important developmental genes across seven embryonic and postnatal stages of brain growth; and the Allen Spinal Cord Atlas, revealing expression for ~20,000 genes in the adult and neonatal mouse spinal cords. Integrated data-mining tools, including reference atlases, informatics analyses, and 3-D viewers, are described. For these massive-scale projects, high-throughput industrial techniques were developed to standardize and reliably repeat experimental goals. To verify consistency and accuracy, a detailed analysis of the 1,000 most viewed genes for the adult mouse brain (according to website page views) was performed by comparing our data with peer-reviewed literature and other databases. We show that our data are highly consistent with independent sources and provide a comprehensive compendium of information and tools used by thousands of researchers each month. All data and tools are freely available via the Allen Brain Atlas portal (www.brain-map.org). PMID:22832508

  16. Comprehensive cellular‐resolution atlas of the adult human brain

    PubMed Central

    Royall, Joshua J.; Sunkin, Susan M.; Ng, Lydia; Facer, Benjamin A.C.; Lesnar, Phil; Guillozet‐Bongaarts, Angie; McMurray, Bergen; Szafer, Aaron; Dolbeare, Tim A.; Stevens, Allison; Tirrell, Lee; Benner, Thomas; Caldejon, Shiella; Dalley, Rachel A.; Dee, Nick; Lau, Christopher; Nyhus, Julie; Reding, Melissa; Riley, Zackery L.; Sandman, David; Shen, Elaine; van der Kouwe, Andre; Varjabedian, Ani; Write, Michelle; Zollei, Lilla; Dang, Chinh; Knowles, James A.; Koch, Christof; Phillips, John W.; Sestan, Nenad; Wohnoutka, Paul; Zielke, H. Ronald; Hohmann, John G.; Jones, Allan R.; Bernard, Amy; Hawrylycz, Michael J.; Hof, Patrick R.; Fischl, Bruce

    2016-01-01

    ABSTRACT Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole‐brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high‐resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion‐weighted imaging (DWI), and 1,356 large‐format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto‐ and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127–3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:27418273

  17. Comprehensive cellular-resolution atlas of the adult human brain.

    PubMed

    Ding, Song-Lin; Royall, Joshua J; Sunkin, Susan M; Ng, Lydia; Facer, Benjamin A C; Lesnar, Phil; Guillozet-Bongaarts, Angie; McMurray, Bergen; Szafer, Aaron; Dolbeare, Tim A; Stevens, Allison; Tirrell, Lee; Benner, Thomas; Caldejon, Shiella; Dalley, Rachel A; Dee, Nick; Lau, Christopher; Nyhus, Julie; Reding, Melissa; Riley, Zackery L; Sandman, David; Shen, Elaine; van der Kouwe, Andre; Varjabedian, Ani; Write, Michelle; Zollei, Lilla; Dang, Chinh; Knowles, James A; Koch, Christof; Phillips, John W; Sestan, Nenad; Wohnoutka, Paul; Zielke, H Ronald; Hohmann, John G; Jones, Allan R; Bernard, Amy; Hawrylycz, Michael J; Hof, Patrick R; Fischl, Bruce; Lein, Ed S

    2016-11-01

    Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole-brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high-resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and 1,356 large-format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto- and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127-3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:27418273

  18. Comprehensive cellular-resolution atlas of the adult human brain.

    PubMed

    Ding, Song-Lin; Royall, Joshua J; Sunkin, Susan M; Ng, Lydia; Facer, Benjamin A C; Lesnar, Phil; Guillozet-Bongaarts, Angie; McMurray, Bergen; Szafer, Aaron; Dolbeare, Tim A; Stevens, Allison; Tirrell, Lee; Benner, Thomas; Caldejon, Shiella; Dalley, Rachel A; Dee, Nick; Lau, Christopher; Nyhus, Julie; Reding, Melissa; Riley, Zackery L; Sandman, David; Shen, Elaine; van der Kouwe, Andre; Varjabedian, Ani; Write, Michelle; Zollei, Lilla; Dang, Chinh; Knowles, James A; Koch, Christof; Phillips, John W; Sestan, Nenad; Wohnoutka, Paul; Zielke, H Ronald; Hohmann, John G; Jones, Allan R; Bernard, Amy; Hawrylycz, Michael J; Hof, Patrick R; Fischl, Bruce; Lein, Ed S

    2016-11-01

    Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole-brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high-resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and 1,356 large-format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto- and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127-3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

  19. An anatomic gene expression atlas of the adult mouse brain.

    PubMed

    Ng, Lydia; Bernard, Amy; Lau, Chris; Overly, Caroline C; Dong, Hong-Wei; Kuan, Chihchau; Pathak, Sayan; Sunkin, Susan M; Dang, Chinh; Bohland, Jason W; Bokil, Hemant; Mitra, Partha P; Puelles, Luis; Hohmann, John; Anderson, David J; Lein, Ed S; Jones, Allan R; Hawrylycz, Michael

    2009-03-01

    Studying gene expression provides a powerful means of understanding structure-function relationships in the nervous system. The availability of genome-scale in situ hybridization datasets enables new possibilities for understanding brain organization based on gene expression patterns. The Anatomic Gene Expression Atlas (AGEA) is a new relational atlas revealing the genetic architecture of the adult C57Bl/6J mouse brain based on spatial correlations across expression data for thousands of genes in the Allen Brain Atlas (ABA). The AGEA includes three discovery tools for examining neuroanatomical relationships and boundaries: (1) three-dimensional expression-based correlation maps, (2) a hierarchical transcriptome-based parcellation of the brain and (3) a facility to retrieve from the ABA specific genes showing enriched expression in local correlated domains. The utility of this atlas is illustrated by analysis of genetic organization in the thalamus, striatum and cerebral cortex. The AGEA is a publicly accessible online computational tool integrated with the ABA (http://mouse.brain-map.org/agea). PMID:19219037

  20. Multiple brain atlas database and atlas-based neuroimaging system.

    PubMed

    Nowinski, W L; Fang, A; Nguyen, B T; Raphel, J K; Jagannathan, L; Raghavan, R; Bryan, R N; Miller, G A

    1997-01-01

    For the purpose of developing multiple, complementary, fully labeled electronic brain atlases and an atlas-based neuroimaging system for analysis, quantification, and real-time manipulation of cerebral structures in two and three dimensions, we have digitized, enhanced, segmented, and labeled the following print brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach and Tournoux, Atlas for Stereotaxy of the Human Brain by Schaltenbrand and Wahren, Referentially Oriented Cerebral MRI Anatomy by Talairach and Tournoux, and Atlas of the Cerebral Sulci by Ono, Kubik, and Abernathey. Three-dimensional extensions of these atlases have been developed as well. All two- and three-dimensional atlases are mutually preregistered and may be interactively registered with an actual patient's data. An atlas-based neuroimaging system has been developed that provides support for reformatting, registration, visualization, navigation, image processing, and quantification of clinical data. The anatomical index contains about 1,000 structures and over 400 sulcal patterns. Several new applications of the brain atlas database also have been developed, supported by various technologies such as virtual reality, the Internet, and electronic publishing. Fusion of information from multiple atlases assists the user in comprehensively understanding brain structures and identifying and quantifying anatomical regions in clinical data. The multiple brain atlas database and atlas-based neuroimaging system have substantial potential impact in stereotactic neurosurgery and radiotherapy by assisting in visualization and real-time manipulation in three dimensions of anatomical structures, in quantitative neuroradiology by allowing interactive analysis of clinical data, in three-dimensional neuroeducation, and in brain function studies.

  1. Towards multimodal atlases of the human brain

    PubMed Central

    Toga, Arthur W.; Thompson, Paul M.; Mori, Susumu; Amunts, Katrin; Zilles, Karl

    2010-01-01

    Atlases of the human brain have an important impact on neuroscience. The emergence of ever more sophisticated imaging techniques, brain mapping methods and analytical strategies has the potential to revolutionize the concept of the brain atlas. Atlases can now combine data describing multiple aspects of brain structure or function at different scales from different subjects, yielding a truly integrative and comprehensive description of this organ. These integrative approaches have provided significant impetus for the human brain mapping initiatives, and have important applications in health and disease. PMID:17115077

  2. The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content.

    PubMed

    Bakker, Rembrandt; Tiesinga, Paul; Kötter, Rolf

    2015-07-01

    The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of brain atlas templates for different species. Its main component is an atlas viewer that displays brain atlas data as a stack of slices in which stereotaxic coordinates and brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when a new slice, coordinate or region is selected. It contains 20 atlas templates in six species, and plugins to compute coordinate transformations, display anatomical connectivity and fiducial points, and retrieve properties, descriptions, definitions and 3d reconstructions of brain regions. The ambition of SBA is to provide a unified representation of all publicly available brain atlases directly in the web browser, while remaining a responsive and light weight resource that specializes in atlas comparisons, searches, coordinate transformations and interactive displays.

  3. Disease-Specific Probabilistic Brain Atlases

    PubMed Central

    Thompson, Paul; Mega, Michael S.; Toga, Arthur W.

    2009-01-01

    Atlases of the human brain, in health and disease, provide a comprehensive framework for understanding brain structure and function. The complexity and variability of brain structure, especially in the gyral patterns of the human cortex, present challenges in creating standardized brain atlases that reflect the anatomy of a population. This paper introduces the concept of a population-based, disease-specific brain atlas that can reflect the unique anatomy and physiology of a particular clinical subpopulation. Based on well-characterized patient groups, disease-specific atlases contain thousands of structure models, composite maps, average templates, and visualizations of structural variability, asymmetry and group-specific differences. They correlate the structural, metabolic, molecular and histologic hallmarks of the disease. Rather than simply fusing information from multiple subjects and sources, new mathematical strategies are introduced to resolve group-specific features not apparent in individual scans. High-dimensional elastic mappings, based on covariant partial differential equations, are developed to encode patterns of cortical variation. In the resulting brain atlas, disease-specific features and regional asymmetries emerge that are not apparent in individual anatomies. The resulting probabilistic atlas can identify patterns of altered structure and function, and can guide algorithms for knowledge-based image analysis, automated image labeling, tissue classification, data mining and functional image analysis. PMID:19424457

  4. A Digital Atlas of the Dog Brain

    PubMed Central

    Datta, Ritobrato; Lee, Jongho; Duda, Jeffrey; Avants, Brian B.; Vite, Charles H.; Tseng, Ben; Gee, James C.; Aguirre, Gustavo D.; Aguirre, Geoffrey K.

    2012-01-01

    There is a long history and a growing interest in the canine as a subject of study in neuroscience research and in translational neurology. In the last few years, anatomical and functional magnetic resonance imaging (MRI) studies of awake and anesthetized dogs have been reported. Such efforts can be enhanced by a population atlas of canine brain anatomy to implement group analyses. Here we present a canine brain atlas derived as the diffeomorphic average of a population of fifteen mesaticephalic dogs. The atlas includes: 1) A brain template derived from in-vivo, T1-weighted imaging at 1 mm isotropic resolution at 3 Tesla (with and without the soft tissues of the head); 2) A co-registered, high-resolution (0.33 mm isotropic) template created from imaging of ex-vivo brains at 7 Tesla; 3) A surface representation of the gray matter/white matter boundary of the high-resolution atlas (including labeling of gyral and sulcal features). The properties of the atlas are considered in relation to historical nomenclature and the evolutionary taxonomy of the Canini tribe. The atlas is available for download (https://cfn.upenn.edu/aguirre/wiki/public:data_plosone_2012_datta). PMID:23284904

  5. Deformably registering and annotating whole CLARITY brains to an atlas via masked LDDMM

    NASA Astrophysics Data System (ADS)

    Kutten, Kwame S.; Vogelstein, Joshua T.; Charon, Nicolas; Ye, Li; Deisseroth, Karl; Miller, Michael I.

    2016-04-01

    The CLARITY method renders brains optically transparent to enable high-resolution imaging in the structurally intact brain. Anatomically annotating CLARITY brains is necessary for discovering which regions contain signals of interest. Manually annotating whole-brain, terabyte CLARITY images is difficult, time-consuming, subjective, and error-prone. Automatically registering CLARITY images to a pre-annotated brain atlas offers a solution, but is difficult for several reasons. Removal of the brain from the skull and subsequent storage and processing cause variable non-rigid deformations, thus compounding inter-subject anatomical variability. Additionally, the signal in CLARITY images arises from various biochemical contrast agents which only sparsely label brain structures. This sparse labeling challenges the most commonly used registration algorithms that need to match image histogram statistics to the more densely labeled histological brain atlases. The standard method is a multiscale Mutual Information B-spline algorithm that dynamically generates an average template as an intermediate registration target. We determined that this method performs poorly when registering CLARITY brains to the Allen Institute's Mouse Reference Atlas (ARA), because the image histogram statistics are poorly matched. Therefore, we developed a method (Mask-LDDMM) for registering CLARITY images, that automatically finds the brain boundary and learns the optimal deformation between the brain and atlas masks. Using Mask-LDDMM without an average template provided better results than the standard approach when registering CLARITY brains to the ARA. The LDDMM pipelines developed here provide a fast automated way to anatomically annotate CLARITY images; our code is available as open source software at http://NeuroData.io.

  6. Interoperable atlases of the human brain.

    PubMed

    Amunts, K; Hawrylycz, M J; Van Essen, D C; Van Horn, J D; Harel, N; Poline, J-B; De Martino, F; Bjaalie, J G; Dehaene-Lambertz, G; Dehaene, S; Valdes-Sosa, P; Thirion, B; Zilles, K; Hill, S L; Abrams, M B; Tass, P A; Vanduffel, W; Evans, A C; Eickhoff, S B

    2014-10-01

    The last two decades have seen an unprecedented development of human brain mapping approaches at various spatial and temporal scales. Together, these have provided a large fundus of information on many different aspects of the human brain including micro- and macrostructural segregation, regional specialization of function, connectivity, and temporal dynamics. Atlases are central in order to integrate such diverse information in a topographically meaningful way. It is noteworthy, that the brain mapping field has been developed along several major lines such as structure vs. function, postmortem vs. in vivo, individual features of the brain vs. population-based aspects, or slow vs. fast dynamics. In order to understand human brain organization, however, it seems inevitable that these different lines are integrated and combined into a multimodal human brain model. To this aim, we held a workshop to determine the constraints of a multi-modal human brain model that are needed to enable (i) an integration of different spatial and temporal scales and data modalities into a common reference system, and (ii) efficient data exchange and analysis. As detailed in this report, to arrive at fully interoperable atlases of the human brain will still require much work at the frontiers of data acquisition, analysis, and representation. Among them, the latter may provide the most challenging task, in particular when it comes to representing features of vastly different scales of space, time and abstraction. The potential benefits of such endeavor, however, clearly outweigh the problems, as only such kind of multi-modal human brain atlas may provide a starting point from which the complex relationships between structure, function, and connectivity may be explored.

  7. Practical MRI atlas of neonatal brain development

    SciTech Connect

    Barkovich, A.J.; Truwit, C.L.

    1990-01-01

    This book is an anatomical reference for cranial magnetic resonance imaging (MRI) studies in neonates and infants. It contains 122 clear, sharp MRI scans and drawings showing changes in the normal appearance of the brain and skull during development. Sections of the atlas depict the major processes of maturation: brain myelination, development of the corpus callosum, development of the cranial bone marrow, and iron deposition in the brain. High-quality scans illustrate how these changes appear on magnetic resonance images during various stages of development.

  8. Atlas warping for brain morphometry

    NASA Astrophysics Data System (ADS)

    Machado, Alexei M. C.; Gee, James C.

    1998-06-01

    In this work, we describe an automated approach to morphometry based on spatial normalizations of the data, and demonstrate its application to the analysis of gender differences in the human corpus callosum. The purpose is to describe a population by a reduced and representative set of variables, from which a prior model can be constructed. Our approach is rooted in the assumption that individual anatomies can be considered as quantitative variations on a common underlying qualitative plane. We can therefore imagine that a given individual's anatomy is a warped version of some referential anatomy, also known as an atlas. The spatial warps which transform a labeled atlas into anatomic alignment with a population yield immediate knowledge about organ size and shape in the group. Furthermore, variation within the set of spatial warps is directly related to the anatomic variation among the subjects. Specifically, the shape statistics--mean and variance of the mappings--for the population can be calculated in a special basis, and an eigendecomposition of the variance performed to identify the most significant modes of shape variation. The results obtained with the corpus callosum study confirm the existence of substantial anatomical differences between males and females, as reported in previous experimental work.

  9. Large scale digital atlases in neuroscience

    NASA Astrophysics Data System (ADS)

    Hawrylycz, M.; Feng, D.; Lau, C.; Kuan, C.; Miller, J.; Dang, C.; Ng, L.

    2014-03-01

    Imaging in neuroscience has revolutionized our current understanding of brain structure, architecture and increasingly its function. Many characteristics of morphology, cell type, and neuronal circuitry have been elucidated through methods of neuroimaging. Combining this data in a meaningful, standardized, and accessible manner is the scope and goal of the digital brain atlas. Digital brain atlases are used today in neuroscience to characterize the spatial organization of neuronal structures, for planning and guidance during neurosurgery, and as a reference for interpreting other data modalities such as gene expression and connectivity data. The field of digital atlases is extensive and in addition to atlases of the human includes high quality brain atlases of the mouse, rat, rhesus macaque, and other model organisms. Using techniques based on histology, structural and functional magnetic resonance imaging as well as gene expression data, modern digital atlases use probabilistic and multimodal techniques, as well as sophisticated visualization software to form an integrated product. Toward this goal, brain atlases form a common coordinate framework for summarizing, accessing, and organizing this knowledge and will undoubtedly remain a key technology in neuroscience in the future. Since the development of its flagship project of a genome wide image-based atlas of the mouse brain, the Allen Institute for Brain Science has used imaging as a primary data modality for many of its large scale atlas projects. We present an overview of Allen Institute digital atlases in neuroscience, with a focus on the challenges and opportunities for image processing and computation.

  10. The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture

    PubMed Central

    Fan, Lingzhong; Li, Hai; Zhuo, Junjie; Zhang, Yu; Wang, Jiaojian; Chen, Liangfu; Yang, Zhengyi; Chu, Congying; Xie, Sangma; Laird, Angela R.; Fox, Peter T.; Eickhoff, Simon B.; Yu, Chunshui; Jiang, Tianzi

    2016-01-01

    The human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. Many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. Using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. The resulting human Brainnetome Atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. Additionally, we further mapped the delineated structures to mental processes by reference to the BrainMap database. It thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. The human Brainnetome Atlas will be made freely available for download at http://atlas.brainnetome.org, so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states. PMID:27230218

  11. The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture.

    PubMed

    Fan, Lingzhong; Li, Hai; Zhuo, Junjie; Zhang, Yu; Wang, Jiaojian; Chen, Liangfu; Yang, Zhengyi; Chu, Congying; Xie, Sangma; Laird, Angela R; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

    2016-08-01

    The human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. Many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. Using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. The resulting human Brainnetome Atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. Additionally, we further mapped the delineated structures to mental processes by reference to the BrainMap database. It thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. The human Brainnetome Atlas will be made freely available for download at http://atlas.brainnetome.org, so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states. PMID:27230218

  12. The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture.

    PubMed

    Fan, Lingzhong; Li, Hai; Zhuo, Junjie; Zhang, Yu; Wang, Jiaojian; Chen, Liangfu; Yang, Zhengyi; Chu, Congying; Xie, Sangma; Laird, Angela R; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

    2016-08-01

    The human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. Many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. Using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. The resulting human Brainnetome Atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. Additionally, we further mapped the delineated structures to mental processes by reference to the BrainMap database. It thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. The human Brainnetome Atlas will be made freely available for download at http://atlas.brainnetome.org, so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states.

  13. The SRI24 multichannel brain atlas: construction and applications

    NASA Astrophysics Data System (ADS)

    Rohlfing, Torsten; Zahr, Natalie M.; Sullivan, Edith V.; Pfefferbaum, Adolf

    2008-03-01

    We present a new standard atlas of the human brain based on magnetic resonance images. The atlas was generated using unbiased population registration from high-resolution images obtained by multichannel-coil acquisition at 3T in a group of 24 normal subjects. The final atlas comprises three anatomical channels (T I-weighted, early and late spin echo), three diffusion-related channels (fractional anisotropy, mean diffusivity, diffusion-weighted image), and three tissue probability maps (CSF, gray matter, white matter). The atlas is dynamic in that it is implicitly represented by nonrigid transformations between the 24 subject images, as well as distortion-correction alignments between the image channels in each subject. The atlas can, therefore, be generated at essentially arbitrary image resolutions and orientations (e.g., AC/PC aligned), without compounding interpolation artifacts. We demonstrate in this paper two different applications of the atlas: (a) region definition by label propagation in a fiber tracking study is enabled by the increased sharpness of our atlas compared with other available atlases, and (b) spatial normalization is enabled by its average shape property. In summary, our atlas has unique features and will be made available to the scientific community as a resource and reference system for future imaging-based studies of the human brain.

  14. Towards an elastographic atlas of brain anatomy.

    PubMed

    Guo, Jing; Hirsch, Sebastian; Fehlner, Andreas; Papazoglou, Sebastian; Scheel, Michael; Braun, Juergen; Sack, Ingolf

    2013-01-01

    Cerebral viscoelastic constants can be measured in a noninvasive, image-based way by magnetic resonance elastography (MRE) for the detection of neurological disorders. However, MRE brain maps of viscoelastic constants are still limited by low spatial resolution. Here we introduce three-dimensional multifrequency MRE of the brain combined with a novel reconstruction algorithm based on a model-free multifrequency inversion for calculating spatially resolved viscoelastic parameter maps of the human brain corresponding to the dynamic range of shear oscillations between 30 and 60 Hz. Maps of two viscoelastic parameters, the magnitude and the phase angle of the complex shear modulus, |G*| and φ, were obtained and normalized to group templates of 23 healthy volunteers in the age range of 22 to 72 years. This atlas of the anatomy of brain mechanics reveals a significant contrast in the stiffness parameter |G*| between different anatomical regions such as white matter (WM; 1.252±0.260 kPa), the corpus callosum genu (CCG; 1.104±0.280 kPa), the thalamus (TH; 1.058±0.208 kPa) and the head of the caudate nucleus (HCN; 0.649±0.101 kPa). φ, which is sensitive to the lossy behavior of the tissue, was in the order of CCG (1.011±0.172), TH (1.037±0.173), CN (0.906±0.257) and WM (0.854±0.169). The proposed method provides the first normalized maps of brain viscoelasticity with anatomical details in subcortical regions and provides useful background data for clinical applications of cerebral MRE.

  15. A three-dimensional digital atlas of the starling brain.

    PubMed

    De Groof, Geert; George, Isabelle; Touj, Sara; Stacho, Martin; Jonckers, Elisabeth; Cousillas, Hugo; Hausberger, Martine; Güntürkün, Onur; Van der Linden, Annemie

    2016-05-01

    Because of their sophisticated vocal behaviour, their social nature, their high plasticity and their robustness, starlings have become an important model species that is widely used in studies of neuroethology of song production and perception. Since magnetic resonance imaging (MRI) represents an increasingly relevant tool for comparative neuroscience, a 3D MRI-based atlas of the starling brain becomes essential. Using multiple imaging protocols we delineated several sensory systems as well as the song control system. This starling brain atlas can easily be used to determine the stereotactic location of identified neural structures at any angle of the head. Additionally, the atlas is useful to find the optimal angle of sectioning for slice experiments, stereotactic injections and electrophysiological recordings. The starling brain atlas is freely available for the scientific community.

  16. Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation.

    PubMed

    Liyanage, Kishan Andre; Steward, Christopher; Moffat, Bradford Armstrong; Opie, Nicholas Lachlan; Rind, Gil Simon; John, Sam Emmanuel; Ronayne, Stephen; May, Clive Newton; O'Brien, Terence John; Milne, Marjorie Eileen; Oxley, Thomas James

    2016-01-01

    Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson's disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution) MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap) to 1 (complete overlap). For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5-0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0-0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access. PMID:27285947

  17. Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation.

    PubMed

    Liyanage, Kishan Andre; Steward, Christopher; Moffat, Bradford Armstrong; Opie, Nicholas Lachlan; Rind, Gil Simon; John, Sam Emmanuel; Ronayne, Stephen; May, Clive Newton; O'Brien, Terence John; Milne, Marjorie Eileen; Oxley, Thomas James

    2016-01-01

    Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson's disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution) MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap) to 1 (complete overlap). For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5-0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0-0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access.

  18. Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation

    PubMed Central

    Steward, Christopher; Moffat, Bradford Armstrong; Opie, Nicholas Lachlan; Rind, Gil Simon; John, Sam Emmanuel; Ronayne, Stephen; May, Clive Newton; O’Brien, Terence John; Milne, Marjorie Eileen; Oxley, Thomas James

    2016-01-01

    Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson’s disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution) MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap) to 1 (complete overlap). For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5–0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0–0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access. PMID:27285947

  19. Whole-brain activity mapping onto a zebrafish brain atlas

    PubMed Central

    Randlett, Owen; Wee, Caroline L.; Naumann, Eva A.; Nnaemeka, Onyeka; Schoppik, David; Fitzgerald, James E.; Portugues, Ruben; Lacoste, Alix M.B.; Riegler, Clemens; Engert, Florian; Schier, Alexander F.

    2015-01-01

    In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open source atlas containing molecular labels and anatomical region definitions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated-Extracellular signal-regulated kinase (ERK/MAPK) as a readout of neural activity, we have developed a system to create and contextualize whole brain maps of stimulus- and behavior-dependent neural activity. This MAP-Mapping (Mitogen Activated Protein kinase – Mapping) assay is technically simple, fast, inexpensive, and data analysis is completely automated. Since MAP-Mapping is performed on fish that are freely swimming, it is applicable to nearly any stimulus or behavior. We demonstrate the utility of our high-throughput approach using hunting/feeding, pharmacological, visual and noxious stimuli. The resultant maps outline hundreds of areas associated with behaviors. PMID:26778924

  20. Whole-brain activity mapping onto a zebrafish brain atlas.

    PubMed

    Randlett, Owen; Wee, Caroline L; Naumann, Eva A; Nnaemeka, Onyeka; Schoppik, David; Fitzgerald, James E; Portugues, Ruben; Lacoste, Alix M B; Riegler, Clemens; Engert, Florian; Schier, Alexander F

    2015-11-01

    In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open-source atlas containing molecular labels and definitions of anatomical regions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated extracellular signal–regulated kinase (ERK) as a readout of neural activity, we have developed a system to create and contextualize whole-brain maps of stimulus- and behavior-dependent neural activity. This mitogen-activated protein kinase (MAP)-mapping assay is technically simple, and data analysis is completely automated. Because MAP-mapping is performed on freely swimming fish, it is applicable to studies of nearly any stimulus or behavior. Here we demonstrate our high-throughput approach using pharmacological, visual and noxious stimuli, as well as hunting and feeding. The resultant maps outline hundreds of areas associated with behaviors. PMID:26778924

  1. Resource atlases for multi-atlas brain segmentations with multiple ontology levels based on T1-weighted MRI.

    PubMed

    Wu, Dan; Ma, Ting; Ceritoglu, Can; Li, Yue; Chotiyanonta, Jill; Hou, Zhipeng; Hsu, John; Xu, Xin; Brown, Timothy; Miller, Michael I; Mori, Susumu

    2016-01-15

    Technologies for multi-atlas brain segmentation of T1-weighted MRI images have rapidly progressed in recent years, with highly promising results. This approach, however, relies on a large number of atlases with accurate and consistent structural identifications. Here, we introduce our atlas inventories (n=90), which cover ages 4-82years with unique hierarchical structural definitions (286 structures at the finest level). This multi-atlas library resource provides the flexibility to choose appropriate atlases for various studies with different age ranges and structure-definition criteria. In this paper, we describe the details of the atlas resources and demonstrate the improved accuracy achievable with a dynamic age-matching approach, in which atlases that most closely match the subject's age are dynamically selected. The advanced atlas creation strategy, together with atlas pre-selection principles, is expected to support the further development of multi-atlas image segmentation. PMID:26499813

  2. Resource atlases for multi-atlas brain segmentations with multiple ontology levels based on T1-weighted MRI.

    PubMed

    Wu, Dan; Ma, Ting; Ceritoglu, Can; Li, Yue; Chotiyanonta, Jill; Hou, Zhipeng; Hsu, John; Xu, Xin; Brown, Timothy; Miller, Michael I; Mori, Susumu

    2016-01-15

    Technologies for multi-atlas brain segmentation of T1-weighted MRI images have rapidly progressed in recent years, with highly promising results. This approach, however, relies on a large number of atlases with accurate and consistent structural identifications. Here, we introduce our atlas inventories (n=90), which cover ages 4-82years with unique hierarchical structural definitions (286 structures at the finest level). This multi-atlas library resource provides the flexibility to choose appropriate atlases for various studies with different age ranges and structure-definition criteria. In this paper, we describe the details of the atlas resources and demonstrate the improved accuracy achievable with a dynamic age-matching approach, in which atlases that most closely match the subject's age are dynamically selected. The advanced atlas creation strategy, together with atlas pre-selection principles, is expected to support the further development of multi-atlas image segmentation.

  3. Combining multi-atlas segmentation with brain surface estimation

    NASA Astrophysics Data System (ADS)

    Huo, Yuankai; Carass, Aaron; Resnick, Susan M.; Pham, Dzung L.; Prince, Jerry L.; Landman, Bennett A.

    2016-03-01

    Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this "segmentation to surface to parcellation" strategy has shown limitation in various situations. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly population.

  4. Combining Multi-atlas Segmentation with Brain Surface Estimation

    PubMed Central

    Carass, Aaron; Resnick, Susan M.; Pham, Dzung L.; Prince, Jerry L.; Landman, Bennett A.

    2016-01-01

    Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this “segmentation to surface to parcellation” strategy has shown limitations in various situations. In this work, we propose a novel “multi-atlas segmentation to surface” method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly

  5. Construction of brain atlases based on a multi-center MRI dataset of 2020 Chinese adults.

    PubMed

    Liang, Peipeng; Shi, Lin; Chen, Nan; Luo, Yishan; Wang, Xing; Liu, Kai; Mok, Vincent C T; Chu, Winnie C W; Wang, Defeng; Li, Kuncheng

    2015-01-01

    Despite the known morphological differences (e.g., brain shape and size) in the brains of populations of different origins (e.g., age and race), the Chinese brain atlas is less studied. In the current study, we developed a statistical brain atlas based on a multi-center high quality magnetic resonance imaging (MRI) dataset of 2020 Chinese adults (18-76 years old). We constructed 12 Chinese brain atlas from the age 20 year to the age 75 at a 5 years interval. New Chinese brain standard space, coordinates, and brain area labels were further defined. The new Chinese brain atlas was validated in brain registration and segmentation. It was found that, as contrast to the MNI152 template, the proposed Chinese atlas showed higher accuracy in hippocampus segmentation and relatively smaller shape deformations during registration. These results indicate that a population-specific time varying brain atlas may be more appropriate for studies involving Chinese populations. PMID:26678304

  6. Intensity and sulci landmark combined brain atlas construction for Chinese pediatric population.

    PubMed

    Luo, Yishan; Shi, Lin; Weng, Jian; He, Hongjian; Chu, Winnie C W; Chen, Feiyan; Wang, Defeng

    2014-08-01

    Constructing an atlas from a population of brain images is of vital importance to medical image analysis. Especially in neuroscience study, creating a brain atlas is useful for intra- and inter-population comparison. Research on brain atlas construction has attracted great attention in recent years, but the research on pediatric population is still limited, mainly due to the limited availability and the relatively low quality of pediatric magnetic resonance brain images. This article is targeted at creating a high quality representative brain atlas for Chinese pediatric population. To achieve this goal, we have designed a set of preprocessing procedures to improve the image quality and developed an intensity and sulci landmark combined groupwise registration method to align the population of images for atlas construction. As demonstrated in experiments, the newly constructed atlas can better represent the size and shape of brains of Chinese pediatric population, and show better performance in Chinese pediatric brain image analysis compared with other standard atlases.

  7. A Tool to Investigate Symmetry Properties of Newborns Brain: The Newborns' Symmetric Brain Atlas

    PubMed Central

    Noorizadeh, Negar; Kazemi, Kamran; Grebe, Reinhard; Helfroush, Mohammad Sadegh; Mahmoudzadeh, Mahdi; Wallois, Fabrice

    2013-01-01

    It is well established that the two hemispheres of the human brain exhibit a certain degree of asymmetry. Postmortem studies of developing brains of pre- and postpartum infants have shown that already in this early stage of development Heschl gyrus, planum temporale and superior temporal sulcus (STS) exhibit pronounced asymmetry. Advances in acquisition and computational evaluation of high-resolution magnetic resonance images provide enhanced tools for noninvasive studies of brain asymmetry in newborns. Until now most atlases used for image processing contain themselves asymmetry and may thus introduce and/or increase asymmetry already contained in the original data of brain structural or functional images. So, it is preferable to avoid the application of these asymmetric atlases. Thus, in this paper we present our framework to create a symmetric brain atlas from a group of newborns aged between 39 and 42 weeks after gestation. The resulting atlas demonstrates no difference between its original and its flipped version as should be the case for an asymmetric atlas. Consequently, the resulting symmetric atlas can be used for applications such as analysis of development of brain asymmetry in the context of language development. PMID:24967308

  8. Stereotactic PET atlas of the human brain: Aid for visual interpretation of functional brain images

    SciTech Connect

    Minoshima, S.; Koeppe, R.A.; Frey, A.; Ishihara, M.; Kuhl, D.E.

    1994-06-01

    In the routine analysis of functional brain images obtained by PET, subjective visual interpretation is often used for anatomic localization. To enhance the accuracy and consistency of the anatomic interpretation, a PET stereotactic atlas and localization approach was designed for functional brain images. The PET atlas was constructed from a high-resolution [{sup 18}F]fluorodeoxyglucose (FDG) image set of a normal volunteer (a 41-yr-ld woman). The image set was reoriented stereotactically, according to the intercommissural (anterior and posterior commissures) line and transformed to the standard stereotactic atlas coordinates. Cerebral structures were annotated on the transaxial planes using a proportional grid system and surface-rendered images. The stereotactic localization technique was applied to image sets from patients with Alzheimer`s disease, and areas of functional alteration were localized visually by referring to the PET atlas. Major brain structures were identified on both transaxial planes and surface-rendered images. In the stereotactic system, anatomic correspondence between the PET atlas and stereotactically reoriented individual image sets of patients with Alzheimer`s disease facilitated both indirect and direct localization of the cerebral structures. Because rapid stereotactic alignment methods for PET images are now available for routine use, the PET atlas will serve as an aid for visual interpretation of functional brain images in the stereotactic system. Widespread application of stereotactic localization may be used in functional brain images, not only in the research setting, but also in routine clinical situations. 41 refs., 3 figs.

  9. The Brain Atlas Concordance Problem: Quantitative Comparison of Anatomical Parcellations

    PubMed Central

    Bohland, Jason W.; Bokil, Hemant; Allen, Cara B.; Mitra, Partha P.

    2009-01-01

    Many neuroscientific reports reference discrete macro-anatomical regions of the brain which were delineated according to a brain atlas or parcellation protocol. Currently, however, no widely accepted standards exist for partitioning the cortex and subcortical structures, or for assigning labels to the resulting regions, and many procedures are being actively used. Previous attempts to reconcile neuroanatomical nomenclatures have been largely qualitative, focusing on the development of thesauri or simple semantic mappings between terms. Here we take a fundamentally different approach, discounting the names of regions and instead comparing their definitions as spatial entities in an effort to provide more precise quantitative mappings between anatomical entities as defined by different atlases. We develop an analytical framework for studying this brain atlas concordance problem, and apply these methods in a comparison of eight diverse labeling methods used by the neuroimaging community. These analyses result in conditional probabilities that enable mapping between regions across atlases, which also form the input to graph-based methods for extracting higher-order relationships between sets of regions and to procedures for assessing the global similarity between different parcellations of the same brain. At a global scale, the overall results demonstrate a considerable lack of concordance between available parcellation schemes, falling within chance levels for some atlas pairs. At a finer level, this study reveals spatial relationships between sets of defined regions that are not obviously apparent; these are of high potential interest to researchers faced with the challenge of comparing results that were based on these different anatomical models, particularly when coordinate-based data are not available. The complexity of the spatial overlap patterns revealed points to problems for attempts to reconcile anatomical parcellations and nomenclatures using strictly

  10. Consistent cortical reconstruction and multi-atlas brain segmentation.

    PubMed

    Huo, Yuankai; Plassard, Andrew J; Carass, Aaron; Resnick, Susan M; Pham, Dzung L; Prince, Jerry L; Landman, Bennett A

    2016-09-01

    Whole brain segmentation and cortical surface reconstruction are two essential techniques for investigating the human brain. Spatial inconsistences, which can hinder further integrated analyses of brain structure, can result due to these two tasks typically being conducted independently of each other. FreeSurfer obtains self-consistent whole brain segmentations and cortical surfaces. It starts with subcortical segmentation, then carries out cortical surface reconstruction, and ends with cortical segmentation and labeling. However, this "segmentation to surface to parcellation" strategy has shown limitations in various cohorts such as older populations with large ventricles. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. A modification called MaCRUISE(+) is designed to perform well when white matter lesions are present. Comparing to the benchmarks CRUISE and FreeSurfer, the surface accuracy of MaCRUISE and MaCRUISE(+) is validated using two independent datasets with expertly placed cortical landmarks. A third independent dataset with expertly delineated volumetric labels is employed to compare segmentation performance. Finally, 200MR volumetric images from an older adult sample are used to assess the robustness of MaCRUISE and FreeSurfer. The advantages of MaCRUISE are: (1) MaCRUISE constructs self-consistent voxelwise segmentations and cortical surfaces, while MaCRUISE(+) is robust to white matter pathology. (2) MaCRUISE achieves more accurate whole brain segmentations than independently conducting the multi-atlas segmentation. (3) MaCRUISE is comparable in accuracy to FreeSurfer (when FreeSurfer does not exhibit global failures) while achieving greater robustness across an older adult population. MaCRUISE has been made freely

  11. Consistent cortical reconstruction and multi-atlas brain segmentation.

    PubMed

    Huo, Yuankai; Plassard, Andrew J; Carass, Aaron; Resnick, Susan M; Pham, Dzung L; Prince, Jerry L; Landman, Bennett A

    2016-09-01

    Whole brain segmentation and cortical surface reconstruction are two essential techniques for investigating the human brain. Spatial inconsistences, which can hinder further integrated analyses of brain structure, can result due to these two tasks typically being conducted independently of each other. FreeSurfer obtains self-consistent whole brain segmentations and cortical surfaces. It starts with subcortical segmentation, then carries out cortical surface reconstruction, and ends with cortical segmentation and labeling. However, this "segmentation to surface to parcellation" strategy has shown limitations in various cohorts such as older populations with large ventricles. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. A modification called MaCRUISE(+) is designed to perform well when white matter lesions are present. Comparing to the benchmarks CRUISE and FreeSurfer, the surface accuracy of MaCRUISE and MaCRUISE(+) is validated using two independent datasets with expertly placed cortical landmarks. A third independent dataset with expertly delineated volumetric labels is employed to compare segmentation performance. Finally, 200MR volumetric images from an older adult sample are used to assess the robustness of MaCRUISE and FreeSurfer. The advantages of MaCRUISE are: (1) MaCRUISE constructs self-consistent voxelwise segmentations and cortical surfaces, while MaCRUISE(+) is robust to white matter pathology. (2) MaCRUISE achieves more accurate whole brain segmentations than independently conducting the multi-atlas segmentation. (3) MaCRUISE is comparable in accuracy to FreeSurfer (when FreeSurfer does not exhibit global failures) while achieving greater robustness across an older adult population. MaCRUISE has been made freely

  12. Windows on the brain: the emerging role of atlases and databases in neuroscience

    NASA Technical Reports Server (NTRS)

    Van Essen, David C.; VanEssen, D. C. (Principal Investigator)

    2002-01-01

    Brain atlases and associated databases have great potential as gateways for navigating, accessing, and visualizing a wide range of neuroscientific data. Recent progress towards realizing this potential includes the establishment of probabilistic atlases, surface-based atlases and associated databases, combined with improvements in visualization capabilities and internet access.

  13. Detail-preserving construction of neonatal brain atlases in space-frequency domain.

    PubMed

    Zhang, Yuyao; Shi, Feng; Yap, Pew-Thian; Shen, Dinggang

    2016-06-01

    Brain atlases are commonly utilized in neuroimaging studies. However, most brain atlases are fuzzy and lack structural details, especially in the cortical regions. This is mainly caused by the image averaging process involved in atlas construction, which often smoothes out high-frequency contents that capture fine anatomical details. Brain atlas construction for neonatal images is even more challenging due to insufficient spatial resolution and low tissue contrast. In this paper, we propose a novel framework for detail-preserving construction of population-representative atlases. Our approach combines spatial and frequency information to better preserve image details. This is achieved by performing atlas construction in the space-frequency domain given by wavelet transform. In particular, sparse patch-based atlas construction is performed in all frequency subbands, and the results are combined to give a final atlas. For enhancing anatomical details, tissue probability maps are also used to guide atlas construction. Experimental results show that our approach can produce atlases with greater structural details than existing atlases. Hum Brain Mapp 37:2133-2150, 2016. © 2016 Wiley Periodicals, Inc.

  14. High-resolution in vivo Wistar rodent brain atlas based on T1 weighted image

    NASA Astrophysics Data System (ADS)

    Huang, Su; Lu, Zhongkang; Huang, Weimin; Seramani, Sankar; Ramasamy, Boominathan; Sekar, Sakthivel; Guan, Cuntai; Bhakoo, Kishore

    2016-03-01

    Image based atlases for rats brain have a significant impact on pre-clinical research. In this project we acquired T1-weighted images from Wistar rodent brains with fine 59μm isotropical resolution for generation of the atlas template image. By applying post-process procedures using a semi-automatic brain extraction method, we delineated the brain tissues from source data. Furthermore, we applied a symmetric group-wise normalization method to generate an optimized template of T1 image of rodent brain, then aligned our template to the Waxholm Space. In addition, we defined several simple and explicit landmarks to corresponding our template with the well known Paxinos stereotaxic reference system. Anchoring at the origin of the Waxholm Space, we applied piece-wise linear transformation method to map the voxels of the template into the coordinates system in Paxinos' stereotoxic coordinates to facilitate the labelling task. We also cross-referenced our data with both published rodent brain atlas and image atlases available online, methodologically labelling the template to produce a Wistar brain atlas identifying more than 130 structures. Particular attention was paid to the cortex and cerebellum, as these areas encompass the most researched aspects of brain functions. Moreover, we adopted the structure hierarchy and naming nomenclature common to various atlases, so that the names and hierarchy structure presented in the atlas are readily recognised for easy use. It is believed the atlas will present a useful tool in rodent brain functional and pharmaceutical studies.

  15. Digital Atlas of the Zebra Finch (Taeniopygia guttata) Brain: a High Resolution Photo Atlas

    PubMed Central

    Karten, Harvey J.; Brzozowska-Prechtl, Agnieszka; Lovell, Peter V.; Tang, Daniel D.; Mello, Claudio V.; Wang, Haibin; Mitra, Partha P.

    2014-01-01

    We describe a set of new comprehensive, high-quality, high-resolution digital images of histological sections from the brain of male zebra finches (Taeniopygia guttata), and make them publicly available through an interactive website (http://zebrafinch.brainarchitecture.org/). These images provide a basis for the production of a dimensionally accurate and detailed digital non-stereotaxic atlas. Nissl- and myelin-stained brain sections are provided in the transverse, sagittal, and horizontal planes, with the transverse plane approximating the more traditional Frankfurt Plane. In addition, a separate set of brain sections in this same plane is stained for tyrosine hydroxylase, revealing the distribution of catecholaminergic neurons (dopaminergic, noradrenergic, and adrenergic) in the songbird brain. For a subset of sagittal sections we have also prepared a corresponding set of drawings, defining and annotating various nuclei, fields, and fiber tracts that are visible under Nissl and myelin staining. This atlas of the zebra finch brain is expected to become an important tool for birdsong research and comparative studies of brain organization and evolution. PMID:23896990

  16. An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases.

    PubMed

    Forbes, Jessica L; Kim, Regina E Y; Paulsen, Jane S; Johnson, Hans J

    2016-01-01

    The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%. PMID:27536233

  17. An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases

    PubMed Central

    Forbes, Jessica L.; Kim, Regina E. Y.; Paulsen, Jane S.; Johnson, Hans J.

    2016-01-01

    The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%. PMID:27536233

  18. An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases.

    PubMed

    Forbes, Jessica L; Kim, Regina E Y; Paulsen, Jane S; Johnson, Hans J

    2016-01-01

    The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%.

  19. Brain atlas deformation in the presence of small and large space-occupying tumors.

    PubMed

    Dawant, B M; Hartmann, S L; Pan, Shiyan; Gadamsetty, S

    2002-01-01

    Brain atlases contain a wealth of information that could be used in radiation therapy or neurosurgical planning. Until now, however, when large space-occupying tumors and lesions drastically alter the shape of brain structures and substructures, atlas-based methods have been of limited use. In this work, we present a new technique that permits a brain atlas to be warped onto image volumes in which large lesions are present. First we show that a method previously used for atlas-based segmentation of normal brains can also be used for brains with small lesions. We then present an extension of this technique for brains with large lesions. This involves several steps: a global registration to bring the two volumes into approximate correspondence; a local registration to warp the atlas onto the patient volume; the seeding of the warped atlas with a tumor model derived from patient data; and the deformation of the seeded atlas. Global registration is performed using a mutual information criterion. The method we have used for atlas warping is derived from optical flow principles. Preliminary results obtained on real patient images are presented. These results indicate that the proposed method can be used to automatically segment structures of interest in brains with gross deformation. Potential areas of application for this method include automatic labeling of critical structures for radiation therapy and presurgical planning. PMID:12173876

  20. 3D brain atlas reconstructor service--online repository of three-dimensional models of brain structures.

    PubMed

    Majka, Piotr; Kowalski, Jakub M; Chlodzinska, Natalia; Wójcik, Daniel K

    2013-10-01

    Brain atlases are important tools of neuroscience. Traditionally prepared in paper book format, more and more commonly they take digital form which extends their utility. To simplify work with different atlases, to lay the ground for developing universal tools which could abstract from the origin of the atlas, efforts are being made to provide common interfaces to these atlases. 3D Brain Atlas Reconstructor service (3dBARs) described here is a repository of digital representations of different brain atlases in CAF format which we recently proposed and a repository of 3D models of brain structures. A graphical front-end is provided for creating and viewing the reconstructed models as well as the underlying 2D atlas data. An application programming interface (API) facilitates programmatic access to the service contents from other websites. From a typical user's point of view, 3dBARs offers an accessible way to mine publicly available atlasing data with a convenient browser based interface, without the need to install extra software. For a developer of services related to brain atlases, 3dBARs supplies mechanisms for enhancing functionality of other software. The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large. The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure. PMID:23943281

  1. A diffusion tensor MRI atlas of the postmortem rhesus macaque brain.

    PubMed

    Calabrese, Evan; Badea, Alexandra; Coe, Christopher L; Lubach, Gabriele R; Shi, Yundi; Styner, Martin A; Johnson, G Allan

    2015-08-15

    The rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate for modeling the structure and function of the brain. Brain atlases, and particularly those based on magnetic resonance imaging (MRI), have become important tools for understanding normal brain structure, and for identifying structural abnormalities resulting from disease states, exposures, and/or aging. Diffusion tensor imaging (DTI)-based MRI brain atlases are widely used in both human and macaque brain imaging studies because of the unique contrasts, quantitative diffusion metrics, and diffusion tractography that they can provide. Previous MRI and DTI atlases of the rhesus brain have been limited by low contrast and/or low spatial resolution imaging. Here we present a microscopic resolution MRI/DTI atlas of the rhesus brain based on 10 postmortem brain specimens. The atlas includes both structural MRI and DTI image data, a detailed three-dimensional segmentation of 241 anatomic structures, diffusion tractography, cortical thickness estimates, and maps of anatomic variability among atlas specimens. This atlas incorporates many useful features from previous work, including anatomic label nomenclature and ontology, data orientation, and stereotaxic reference frame, and further extends prior analyses with the inclusion of high-resolution multi-contrast image data.

  2. Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline.

    PubMed

    Wang, Jiahui; Vachet, Clement; Rumple, Ashley; Gouttard, Sylvain; Ouziel, Clémentine; Perrot, Emilie; Du, Guangwei; Huang, Xuemei; Gerig, Guido; Styner, Martin

    2014-01-01

    Automated segmenting and labeling of individual brain anatomical regions, in MRI are challenging, due to the issue of individual structural variability. Although atlas-based segmentation has shown its potential for both tissue and structure segmentation, due to the inherent natural variability as well as disease-related changes in MR appearance, a single atlas image is often inappropriate to represent the full population of datasets processed in a given neuroimaging study. As an alternative for the case of single atlas segmentation, the use of multiple atlases alongside label fusion techniques has been introduced using a set of individual "atlases" that encompasses the expected variability in the studied population. In our study, we proposed a multi-atlas segmentation scheme with a novel graph-based atlas selection technique. We first paired and co-registered all atlases and the subject MR scans. A directed graph with edge weights based on intensity and shape similarity between all MR scans is then computed. The set of neighboring templates is selected via clustering of the graph. Finally, weighted majority voting is employed to create the final segmentation over the selected atlases. This multi-atlas segmentation scheme is used to extend a single-atlas-based segmentation toolkit entitled AutoSeg, which is an open-source, extensible C++ based software pipeline employing BatchMake for its pipeline scripting, developed at the Neuro Image Research and Analysis Laboratories of the University of North Carolina at Chapel Hill. AutoSeg performs N4 intensity inhomogeneity correction, rigid registration to a common template space, automated brain tissue classification based skull-stripping, and the multi-atlas segmentation. The multi-atlas-based AutoSeg has been evaluated on subcortical structure segmentation with a testing dataset of 20 adult brain MRI scans and 15 atlas MRI scans. The AutoSeg achieved mean Dice coefficients of 81.73% for the subcortical structures. PMID

  3. BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy.

    PubMed

    Mikula, Shawn; Stone, James M; Jones, Edward G

    2008-01-01

    BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo sapiens, Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, and Tyto alba, are accessible online. The methods and tools we describe are useful for both research and teaching, and can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. These tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level, and can facilitate large-scale connectional tracing, histochemical and stereological analyses. PMID:19129928

  4. Regional growth and atlasing of the developing human brain.

    PubMed

    Makropoulos, Antonios; Aljabar, Paul; Wright, Robert; Hüning, Britta; Merchant, Nazakat; Arichi, Tomoki; Tusor, Nora; Hajnal, Joseph V; Edwards, A David; Counsell, Serena J; Rueckert, Daniel

    2016-01-15

    Detailed morphometric analysis of the neonatal brain is required to characterise brain development and define neuroimaging biomarkers related to impaired brain growth. Accurate automatic segmentation of neonatal brain MRI is a prerequisite to analyse large datasets. We have previously presented an accurate and robust automatic segmentation technique for parcellating the neonatal brain into multiple cortical and subcortical regions. In this study, we further extend our segmentation method to detect cortical sulci and provide a detailed delineation of the cortical ribbon. These detailed segmentations are used to build a 4-dimensional spatio-temporal structural atlas of the brain for 82 cortical and subcortical structures throughout this developmental period. We employ the algorithm to segment an extensive database of 420 MR images of the developing brain, from 27 to 45weeks post-menstrual age at imaging. Regional volumetric and cortical surface measurements are derived and used to investigate brain growth and development during this critical period and to assess the impact of immaturity at birth. Whole brain volume, the absolute volume of all structures studied, cortical curvature and cortical surface area increased with increasing age at scan. Relative volumes of cortical grey matter, cerebellum and cerebrospinal fluid increased with age at scan, while relative volumes of white matter, ventricles, brainstem and basal ganglia and thalami decreased. Preterm infants at term had smaller whole brain volumes, reduced regional white matter and cortical and subcortical grey matter volumes, and reduced cortical surface area compared with term born controls, while ventricular volume was greater in the preterm group. Increasing prematurity at birth was associated with a reduction in total and regional white matter, cortical and subcortical grey matter volume, an increase in ventricular volume, and reduced cortical surface area. PMID:26499811

  5. Regional growth and atlasing of the developing human brain.

    PubMed

    Makropoulos, Antonios; Aljabar, Paul; Wright, Robert; Hüning, Britta; Merchant, Nazakat; Arichi, Tomoki; Tusor, Nora; Hajnal, Joseph V; Edwards, A David; Counsell, Serena J; Rueckert, Daniel

    2016-01-15

    Detailed morphometric analysis of the neonatal brain is required to characterise brain development and define neuroimaging biomarkers related to impaired brain growth. Accurate automatic segmentation of neonatal brain MRI is a prerequisite to analyse large datasets. We have previously presented an accurate and robust automatic segmentation technique for parcellating the neonatal brain into multiple cortical and subcortical regions. In this study, we further extend our segmentation method to detect cortical sulci and provide a detailed delineation of the cortical ribbon. These detailed segmentations are used to build a 4-dimensional spatio-temporal structural atlas of the brain for 82 cortical and subcortical structures throughout this developmental period. We employ the algorithm to segment an extensive database of 420 MR images of the developing brain, from 27 to 45weeks post-menstrual age at imaging. Regional volumetric and cortical surface measurements are derived and used to investigate brain growth and development during this critical period and to assess the impact of immaturity at birth. Whole brain volume, the absolute volume of all structures studied, cortical curvature and cortical surface area increased with increasing age at scan. Relative volumes of cortical grey matter, cerebellum and cerebrospinal fluid increased with age at scan, while relative volumes of white matter, ventricles, brainstem and basal ganglia and thalami decreased. Preterm infants at term had smaller whole brain volumes, reduced regional white matter and cortical and subcortical grey matter volumes, and reduced cortical surface area compared with term born controls, while ventricular volume was greater in the preterm group. Increasing prematurity at birth was associated with a reduction in total and regional white matter, cortical and subcortical grey matter volume, an increase in ventricular volume, and reduced cortical surface area.

  6. Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline

    PubMed Central

    Wang, Jiahui; Vachet, Clement; Rumple, Ashley; Gouttard, Sylvain; Ouziel, Clémentine; Perrot, Emilie; Du, Guangwei; Huang, Xuemei; Gerig, Guido; Styner, Martin

    2014-01-01

    Automated segmenting and labeling of individual brain anatomical regions, in MRI are challenging, due to the issue of individual structural variability. Although atlas-based segmentation has shown its potential for both tissue and structure segmentation, due to the inherent natural variability as well as disease-related changes in MR appearance, a single atlas image is often inappropriate to represent the full population of datasets processed in a given neuroimaging study. As an alternative for the case of single atlas segmentation, the use of multiple atlases alongside label fusion techniques has been introduced using a set of individual “atlases” that encompasses the expected variability in the studied population. In our study, we proposed a multi-atlas segmentation scheme with a novel graph-based atlas selection technique. We first paired and co-registered all atlases and the subject MR scans. A directed graph with edge weights based on intensity and shape similarity between all MR scans is then computed. The set of neighboring templates is selected via clustering of the graph. Finally, weighted majority voting is employed to create the final segmentation over the selected atlases. This multi-atlas segmentation scheme is used to extend a single-atlas-based segmentation toolkit entitled AutoSeg, which is an open-source, extensible C++ based software pipeline employing BatchMake for its pipeline scripting, developed at the Neuro Image Research and Analysis Laboratories of the University of North Carolina at Chapel Hill. AutoSeg performs N4 intensity inhomogeneity correction, rigid registration to a common template space, automated brain tissue classification based skull-stripping, and the multi-atlas segmentation. The multi-atlas-based AutoSeg has been evaluated on subcortical structure segmentation with a testing dataset of 20 adult brain MRI scans and 15 atlas MRI scans. The AutoSeg achieved mean Dice coefficients of 81.73% for the subcortical structures

  7. Space-Frequency Detail-Preserving Construction of Neonatal Brain Atlases

    PubMed Central

    Zhang, Yuyao; Shi, Feng; Yap, Pew-Thian; Shen, Dinggang

    2016-01-01

    Brain atlases are an integral component of neuroimaging studies. However, most brain atlases are fuzzy and lack structural details, especially in the cortical regions. In particular, neonatal brain atlases are especially challenging to construct due to the low spatial resolution and low tissue contrast. This is mainly caused by the image averaging process involved in atlas construction, often smoothing out high-frequency contents that indicate fine anatomical details. In this paper, we propose a novel framework for detail-preserving construction of atlases. Our approach combines space and frequency information to better preserve image details. This is achieved by performing reconstruction in the space-frequency domain given by wavelet transform. Sparse patch-based atlas reconstruction is performed in each frequency subband. Combining the results for all these subbands will then result in a refined atlas. Compared with existing atlases, experimental results indicate that our approach has the ability to build an atlas with more structural details, thus leading to better performance when used to normalize a group of testing neonatal images. PMID:27169138

  8. Genomic connectivity networks based on the BrainSpan atlas of the developing human brain

    NASA Astrophysics Data System (ADS)

    Mahfouz, Ahmed; Ziats, Mark N.; Rennert, Owen M.; Lelieveldt, Boudewijn P. F.; Reinders, Marcel J. T.

    2014-03-01

    The human brain comprises systems of networks that span the molecular, cellular, anatomic and functional levels. Molecular studies of the developing brain have focused on elucidating networks among gene products that may drive cellular brain development by functioning together in biological pathways. On the other hand, studies of the brain connectome attempt to determine how anatomically distinct brain regions are connected to each other, either anatomically (diffusion tensor imaging) or functionally (functional MRI and EEG), and how they change over development. A global examination of the relationship between gene expression and connectivity in the developing human brain is necessary to understand how the genetic signature of different brain regions instructs connections to other regions. Furthermore, analyzing the development of connectivity networks based on the spatio-temporal dynamics of gene expression provides a new insight into the effect of neurodevelopmental disease genes on brain networks. In this work, we construct connectivity networks between brain regions based on the similarity of their gene expression signature, termed "Genomic Connectivity Networks" (GCNs). Genomic connectivity networks were constructed using data from the BrainSpan Transcriptional Atlas of the Developing Human Brain. Our goal was to understand how the genetic signatures of anatomically distinct brain regions relate to each other across development. We assessed the neurodevelopmental changes in connectivity patterns of brain regions when networks were constructed with genes implicated in the neurodevelopmental disorder autism (autism spectrum disorder; ASD). Using graph theory metrics to characterize the GCNs, we show that ASD-GCNs are relatively less connected later in development with the cerebellum showing a very distinct expression of ASD-associated genes compared to other brain regions.

  9. A combined histological and MRI brain atlas of the common marmoset monkey, Callithrix jacchus.

    PubMed

    Newman, John D; Kenkel, William M; Aronoff, Emily C; Bock, Nicholas A; Zametkin, Molly R; Silva, Afonso C

    2009-12-11

    The common marmoset, Callithrix jacchus, is of growing importance for research in neuroscience and related fields. In the present work, we describe a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. The histological sections and a simplified schematic atlas are available online at http://udn.nichd.nih.gov/brainatlas_home.html.

  10. Atlas-based segmentation of pathological MR brain images using a model of lesion growth.

    PubMed

    Cuadra, Meritxell Bach; Pollo, Claudio; Bardera, Anton; Cuisenaire, Olivier; Villemure, Jean-Guy; Thiran, Jean-Philippe

    2004-10-01

    We propose a method for brain atlas deformation in the presence of large space-occupying tumors, based on an a priori model of lesion growth that assumes radial expansion of the lesion from its starting point. Our approach involves three steps. First, an affine registration brings the atlas and the patient into global correspondence. Then, the seeding of a synthetic tumor into the brain atlas provides a template for the lesion. The last step is the deformation of the seeded atlas, combining a method derived from optical flow principles and a model of lesion growth. Results show that a good registration is performed and that the method can be applied to automatic segmentation of structures and substructures in brains with gross deformation, with important medical applications in neurosurgery, radiosurgery, and radiotherapy. PMID:15493697

  11. Surface reconstruction from volume data used for creating an adaptable functional brain atlas

    SciTech Connect

    Thurfjell, L. |; Bengtsson, E.

    1995-08-01

    Functions for creating adaptable atlas structures from volume data have now been included in the Karolinska Computerized Brain Atlas (CBA) software system. The main objective is to allow the user to create functional structures based on data from brain activation studies with Positron Emission Tomography (PET). The new structures will be related to the anatomy of the CBA data base brain. Thus, when the atlas is adapted to the anatomy of an individual, the new functional structures will be affected by the same transformation and can therefore be selected and displayed in relation to the anatomy of the individual. In this paper, the different steps involved in the creation of new atlas structures are explained and algorithms and data representations are described. The methods have been tested on data from activation studies. Such a study is chosen to illustrate how the proposed approach can be used.

  12. Automatic tissue segmentation of neonate brain MR Images with subject-specific atlases

    NASA Astrophysics Data System (ADS)

    Cherel, Marie; Budin, Francois; Prastawa, Marcel; Gerig, Guido; Lee, Kevin; Buss, Claudia; Lyall, Amanda; Zaldarriaga Consing, Kirsten; Styner, Martin

    2015-03-01

    Automatic tissue segmentation of the neonate brain using Magnetic Resonance Images (MRI) is extremely important to study brain development and perform early diagnostics but is challenging due to high variability and inhomogeneity in contrast throughout the image due to incomplete myelination of the white matter tracts. For these reasons, current methods often totally fail or give unsatisfying results. Furthermore, most of the subcortical midbrain structures are misclassified due to a lack of contrast in these regions. We have developed a novel method that creates a probabilistic subject-specific atlas based on a population atlas currently containing a number of manually segmented cases. The generated subject-specific atlas is sharp and adapted to the subject that is being processed. We then segment brain tissue classes using the newly created atlas with a single-atlas expectation maximization based method. Our proposed method leads to a much lower failure rate in our experiments. The overall segmentation results are considerably improved when compared to using a non-subject-specific, population average atlas. Additionally, we have incorporated diffusion information obtained from Diffusion Tensor Images (DTI) to improve the detection of white matter that is not visible at this early age in structural MRI (sMRI) due to a lack of myelination. Although this necessitates the acquisition of an additional sequence, the diffusion information improves the white matter segmentation throughout the brain, especially for the mid-brain structures such as the corpus callosum and the internal capsule.

  13. Automatic Tissue Segmentation of Neonate Brain MR Images with Subject-specific Atlases

    PubMed Central

    Cherel, Marie; Budin, Francois; Prastawa, Marcel; Gerig, Guido; Lee, Kevin; Buss, Claudia; Lyall, Amanda; Consing, Kirsten Zaldarriaga; Styner, Martin

    2015-01-01

    Automatic tissue segmentation of the neonate brain using Magnetic Resonance Images (MRI) is extremely important to study brain development and perform early diagnostics but is challenging due to high variability and inhomogeneity in contrast throughout the image due to incomplete myelination of the white matter tracts. For these reasons, current methods often totally fail or give unsatisfying results. Furthermore, most of the subcortical midbrain structures are misclassified due to a lack of contrast in these regions. We have developed a novel method that creates a probabilistic subject-specific atlas based on a population atlas currently containing a number of manually segmented cases. The generated subject-specific atlas is sharp and adapted to the subject that is being processed. We then segment brain tissue classes using the newly created atlas with a single-atlas expectation maximization based method. Our proposed method leads to a much lower failure rate in our experiments. The overall segmentation results are considerably improved when compared to using a non-subject-specific, population average atlas. Additionally, we have incorporated diffusion information obtained from Diffusion Tensor Images (DTI) to improve the detection of white matter that is not visible at this early age in structural MRI (sMRI) due to a lack of myelination. Although this necessitates the acquisition of an additional sequence, the diffusion information improves the white matter segmentation throughout the brain, especially for the mid-brain structures such as the corpus callosum and the internal capsule. PMID:26089584

  14. Three-dimensional atlas of iron, copper, and zinc in the mouse cerebrum and brainstem.

    PubMed

    Hare, Dominic J; Lee, Jason K; Beavis, Alison D; van Gramberg, Amanda; George, Jessica; Adlard, Paul A; Finkelstein, David I; Doble, Philip A

    2012-05-01

    Atlases depicting molecular and functional features of the brain are becoming an integral part of modern neuroscience. In this study we used laser ablation-inductively coupled plasma-mass spectrometry (LA-ICPMS) to quantitatively measure iron (Fe), copper (Cu), and zinc (Zn) levels in a serially sectioned C57BL/6 mouse brain (cerebrum and brainstem). Forty-six sections were analyzed in a single experiment of approximately 158 h in duration. We constructed a 46-plate reference atlas by aligning quantified images of metal distribution with corresponding coronal sections from the Allen Mouse Brain Reference Atlas. The 46 plates were also used to construct three-dimensional models of Fe, Cu, and Zn distribution. This atlas represents the first reconstruction of quantitative trace metal distribution through the brain by LA-ICPMS and will facilitate the study of trace metals in the brain and help to elucidate their role in neurobiology.

  15. A Multidimensional Magnetic Resonance Histology Atlas of the Wistar Rat Brain

    PubMed Central

    Johnson, G. Allan; Calabrese, Evan; Badea, Alexandra; Paxinos, George; Watson, Charles

    2012-01-01

    We have produced a multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). This MR atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. PMID:22634863

  16. Subject Specific Sparse Dictionary Learning for Atlas Based Brain MRI Segmentation

    PubMed Central

    Roy, Snehashis; He, Qing; Sweeney, Elizabeth; Carass, Aaron; Reich, Daniel S.; Prince, Jerry L.; Pham, Dzung L.

    2015-01-01

    Quantitative measurements from segmentations of human brain magnetic resonance (MR) images provide important biomarkers for normal aging and disease progression. In this paper, we propose a patch-based tissue classification method from MR images that uses a sparse dictionary learning approach and atlas priors. Training data for the method consists of an atlas MR image, prior information maps depicting where different tissues are expected to be located, and a hard segmentation. Unlike most atlas-based classification methods that require deformable registration of the atlas priors to the subject, only affine registration is required between the subject and training atlas. A subject specific patch dictionary is created by learning relevant patches from the atlas. Then the subject patches are modeled as sparse combinations of learned atlas patches leading to tissue memberships at each voxel. The combination of prior information in an example-based framework enables us to distinguish tissues having similar intensities but different spatial locations. We demonstrate the efficacy of the approach on the application of whole brain tissue segmentation in subjects with healthy anatomy and normal pressure hydrocephalus, as well as lesion segmentation in multiple sclerosis patients. For each application, quantitative comparisons are made against publicly available, state-of-the art approaches. PMID:26340685

  17. Subject-Specific Sparse Dictionary Learning for Atlas-Based Brain MRI Segmentation.

    PubMed

    Roy, Snehashis; He, Qing; Sweeney, Elizabeth; Carass, Aaron; Reich, Daniel S; Prince, Jerry L; Pham, Dzung L

    2015-09-01

    Quantitative measurements from segmentations of human brain magnetic resonance (MR) images provide important biomarkers for normal aging and disease progression. In this paper, we propose a patch-based tissue classification method from MR images that uses a sparse dictionary learning approach and atlas priors. Training data for the method consists of an atlas MR image, prior information maps depicting where different tissues are expected to be located, and a hard segmentation. Unlike most atlas-based classification methods that require deformable registration of the atlas priors to the subject, only affine registration is required between the subject and training atlas. A subject-specific patch dictionary is created by learning relevant patches from the atlas. Then the subject patches are modeled as sparse combinations of learned atlas patches leading to tissue memberships at each voxel. The combination of prior information in an example-based framework enables us to distinguish tissues having similar intensities but different spatial locations. We demonstrate the efficacy of the approach on the application of whole-brain tissue segmentation in subjects with healthy anatomy and normal pressure hydrocephalus, as well as lesion segmentation in multiple sclerosis patients. For each application, quantitative comparisons are made against publicly available state-of-the art approaches.

  18. 3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain

    PubMed Central

    Rumple, Ashley; McMurray, Matthew; Johns, Josephine; Lauder, Jean; Makam, Pooja; Radcliffe, Marlana; Oguz, Ipek

    2013-01-01

    Anatomical atlases play an important role in the analysis of neuroimaging data in rodent neuroimaging studies. Having a high resolution, detailed atlas not only can expand understanding of rodent brain anatomy, but also enables automatic segmentation of new images, thus greatly increasing the efficiency of future analysis when applied to new data. These atlases can be used to analyze new scans of individual cases using a variety of automated segmentation methods. This project seeks to develop a set of detailed 3D anatomical atlases of the brain at postnatal day 5 (P5), 14 (P14), and adults (P72) in Sprague-Dawley rats. Our methods consisted of first creating a template image based on fixed scans of control rats, then manually segmenting various individual brain regions on the template. Using itk-SNAP software, subcortical and cortical regions, including both white matter and gray matter structures, were manually segmented in the axial, sagittal, and coronal planes. The P5, P14, and P72 atlases had 39, 45, and 29 regions segmented, respectively. These atlases have been made available to the broader research community. PMID:23861758

  19. Brain atlas of the Mongolian gerbil (Meriones unguiculatus) in CT/MRI-aided stereotaxic coordinates.

    PubMed

    Radtke-Schuller, Susanne; Schuller, Gerd; Angenstein, Frank; Grosser, Oliver S; Goldschmidt, Jürgen; Budinger, Eike

    2016-09-01

    A new stereotaxic brain atlas of the Mongolian gerbil (Meriones unguiculatus), an important animal model in neurosciences, is presented. It combines high-quality histological material for identification of brain structures with reliable stereotaxic coordinates. The atlas consists of high-resolution images of frontal sections alternately stained for cell bodies (Nissl) and myelinated fibers (Gallyas) of 62 rostro-caudal levels at intervals of 350 μm. Brain structures were named according to the Paxinos nomenclature for rodents. The accuracy of the stereotaxic coordinate system was improved substantially by comparing and matching the series of histological sections to in vivo brain images of the gerbil obtained by magnetic resonance imaging (MRI). The skull outlines corresponding to the MR images were acquired using X-ray computerized tomography (CT) and were used to establish the relationship between coordinates of brain structures and skull. Landmarks such as lambda, bregma, ear canals and occipital crest can be used to line up skull and brain in standard atlas coordinates. An easily reproducible protocol allows sectioning of experimental brains in the standard frontal plane of the atlas.

  20. Brain atlas of the Mongolian gerbil (Meriones unguiculatus) in CT/MRI-aided stereotaxic coordinates.

    PubMed

    Radtke-Schuller, Susanne; Schuller, Gerd; Angenstein, Frank; Grosser, Oliver S; Goldschmidt, Jürgen; Budinger, Eike

    2016-09-01

    A new stereotaxic brain atlas of the Mongolian gerbil (Meriones unguiculatus), an important animal model in neurosciences, is presented. It combines high-quality histological material for identification of brain structures with reliable stereotaxic coordinates. The atlas consists of high-resolution images of frontal sections alternately stained for cell bodies (Nissl) and myelinated fibers (Gallyas) of 62 rostro-caudal levels at intervals of 350 μm. Brain structures were named according to the Paxinos nomenclature for rodents. The accuracy of the stereotaxic coordinate system was improved substantially by comparing and matching the series of histological sections to in vivo brain images of the gerbil obtained by magnetic resonance imaging (MRI). The skull outlines corresponding to the MR images were acquired using X-ray computerized tomography (CT) and were used to establish the relationship between coordinates of brain structures and skull. Landmarks such as lambda, bregma, ear canals and occipital crest can be used to line up skull and brain in standard atlas coordinates. An easily reproducible protocol allows sectioning of experimental brains in the standard frontal plane of the atlas. PMID:27507296

  1. Atlas-based segmentation of deep brain structures using non-rigid registration

    NASA Astrophysics Data System (ADS)

    Khan, Muhammad Faisal; Mewes, Klaus; Gross, Robert E.; Škrinjar, Oskar

    2008-03-01

    Deep brain structures are frequently used as targets in neurosurgical procedures. However, the boundaries of these structures are often not visible in clinically used MR and CT images. Techniques based on anatomical atlases and indirect targeting are used to infer the location of these targets intraoperatively. Initial errors of such approaches may be up to a few millimeters, which is not negligible. E.g. subthalamic nucleus is approximately 4x6 mm in the axial plane and the diameter of globus pallidus internus is approximately 8 mm, both of which are used as targets in deep brain stimulation surgery. To increase the initial localization accuracy of deep brain structures we have developed an atlas-based segmentation method that can be used for the surgery planning. The atlas is a high resolution MR head scan of a healthy volunteer with nine deep brain structures manually segmented. The quality of the atlas image allowed for the segmentation of the deep brain structures, which is not possible from the clinical MR head scans of patients. The subject image is non-rigidly registered to the atlas image using thin plate splines to represent the transformation and normalized mutual information as a similarity measure. The obtained transformation is used to map the segmented structures from the atlas to the subject image. We tested the approach on five subjects. The quality of the atlas-based segmentation was evaluated by visual inspection of the third and lateral ventricles, putamena, and caudate nuclei, which are visible in the subject MR images. The agreement of these structures for the five tested subjects was approximately 1 to 2 mm.

  2. Atlas to patient registration with brain tumor based on a mesh-free method.

    PubMed

    Diaz, Idanis; Boulanger, Pierre

    2015-08-01

    Brain atlas to patient registration in the presence of tumors is a challenging task because its presence cause brain structure deformations and introduce large intensity variation between the affected areas. This large dissimilarity affects the results of traditional registration methods based on intensity or shape similarities. In order to overcome these problems, we propose a novel method that brings closer the atlas and the patient's image by simulating the mechanical behavior of brain deformation under a tumor pressure. The proposed method use a mesh-free total Lagrangian Explicit Dynamic algorithm for the simulation of atlas deformation and a data driven model of the tumor using multi-modal MRI segmentation. Experimental results look structurally very similar to the patient's image and outperform two of the top ranking algorithms.

  3. A generative probability model of joint label fusion for multi-atlas based brain segmentation

    PubMed Central

    Wu, Guorong; Wang, Qian; Zhang, Daoqiang; Nie, Feiping; Huang, Heng; Shen, Dinggang

    2013-01-01

    Automated labeling of anatomical structures in medical images is very important in many neuroscience studies. Recently, patch-based labeling has been widely investigated to alleviate the possible mis-alignment when registering atlases to the target image. However, the weights used for label fusion from the registered atlases are generally computed independently and thus lack the capability of preventing the ambiguous atlas patches from contributing to the label fusion. More critically, these weights are often calculated based only on the simple patch similarity, thus not necessarily providing optimal solution for label fusion. To address these limitations, we propose a generative probability model to describe the procedure of label fusion in a multi-atlas scenario, for the goal of labeling each point in the target image by the best representative atlas patches that also have the largest labeling unanimity in labeling the underlying point correctly. Specifically, sparsity constraint is imposed upon label fusion weights, in order to select a small number of atlas patches that best represent the underlying target patch, thus reducing the risks of including the misleading atlas patches. The labeling unanimity among atlas patches is achieved by exploring their dependencies, where we model these dependencies as the joint probability of each pair of atlas patches in correctly predicting the labels, by analyzing the correlation of their morphological error patterns and also the labeling consensus among atlases. The patch dependencies will be further recursively updated based on the latest labeling results to correct the possible labeling errors, which falls to the Expectation Maximization (EM) framework. To demonstrate the labeling performance, we have comprehensively evaluated our patch-based labeling method on the whole brain parcellation and hippocampus segmentation. Promising labeling results have been achieved with comparison to the conventional patch-based labeling

  4. A Web-based Brain Atlas of the Vervet Monkey, Chlorocebus aethiops

    PubMed Central

    Woods, Roger P.; Fears, Scott C.; Jorgensen, Matthew J.; Fairbanks, Lynn A.; Toga, Arthur W.; Freimer, Nelson B.

    2010-01-01

    Vervet monkeys are a frequently studied animal model in neuroscience research. Although equally distantly related to humans, the ancestors of vervets diverged from those of macaques and baboons more than eleven million years ago, antedating the divergence of the ancestors of humans, chimpanzees and gorillas. To facilitate anatomic localization in the vervet brain, two linked on-line electronic atlases are described, one based on registered MRI scans from hundreds of vervets (http://www.loni.ucla.edu/Research/Atlases/Data/vervet/vervetmratlas/vervetmratlas.html) and the other based on a high-resolution cryomacrotome study of a single vervet (http://www.loni.ucla.edu/Research/Atlases/Data/vervet/vervetatlas/vervetatlas.html). The averaged MRI atlas is also available as a volume in Neuroimaging Informatics Technology Initiative format. In the cryomacrotome atlas, various sulcal and subcortical structures have been anatomically labeled and surface rendered views are provided along the primary planes of section. Both atlases simultaneously provide views in all three primary planes of section, rapid navigation by clicking on the displayed images, and stereotaxic coordinates in the averaged MRI atlas space. Despite the extended time period since their divergence, the major sulcal and subcortical landmarks in vervets are highly conserved relative to those described in macaques. PMID:20923706

  5. High-resolution digital brain atlases: a Hubble telescope for the brain.

    PubMed

    Jones, Edward G; Stone, James M; Karten, Harvey J

    2011-05-01

    We describe implementation of a method for digitizing at microscopic resolution brain tissue sections containing normal and experimental data and for making the content readily accessible online. Web-accessible brain atlases and virtual microscopes for online examination can be developed using existing computer and internet technologies. Resulting databases, made up of hierarchically organized, multiresolution images, enable rapid, seamless navigation through the vast image datasets generated by high-resolution scanning. Tools for visualization and annotation of virtual microscope slides enable remote and universal data sharing. Interactive visualization of a complete series of brain sections digitized at subneuronal levels of resolution offers fine grain and large-scale localization and quantification of many aspects of neural organization and structure. The method is straightforward and replicable; it can increase accessibility and facilitate sharing of neuroanatomical data. It provides an opportunity for capturing and preserving irreplaceable, archival neurohistological collections and making them available to all scientists in perpetuity, if resources could be obtained from hitherto uninterested agencies of scientific support. PMID:21599693

  6. Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings.

    PubMed

    Mahfouz, Ahmed; van de Giessen, Martijn; van der Maaten, Laurens; Huisman, Sjoerd; Reinders, Marcel; Hawrylycz, Michael J; Lelieveldt, Boudewijn P F

    2015-02-01

    The Allen Brain Atlases enable the study of spatially resolved, genome-wide gene expression patterns across the mammalian brain. Several explorative studies have applied linear dimensionality reduction methods such as Principal Component Analysis (PCA) and classical Multi-Dimensional Scaling (cMDS) to gain insight into the spatial organization of these expression patterns. In this paper, we describe a non-linear embedding technique called Barnes-Hut Stochastic Neighbor Embedding (BH-SNE) that emphasizes the local similarity structure of high-dimensional data points. By applying BH-SNE to the gene expression data from the Allen Brain Atlases, we demonstrate the consistency of the 2D, non-linear embedding of the sagittal and coronal mouse brain atlases, and across 6 human brains. In addition, we quantitatively show that BH-SNE maps are superior in their separation of neuroanatomical regions in comparison to PCA and cMDS. Finally, we assess the effect of higher-order principal components on the global structure of the BH-SNE similarity maps. Based on our observations, we conclude that BH-SNE maps with or without prior dimensionality reduction (based on PCA) provide comprehensive and intuitive insights in both the local and global spatial transcriptome structure of the human and mouse Allen Brain Atlases.

  7. Integrating Retraction Modeling Into an Atlas-Based Framework for Brain Shift Prediction

    PubMed Central

    Chen, Ishita; Ong, Rowena E.; Simpson, Amber L.; Sun, Kay; Thompson, Reid C.

    2015-01-01

    In recent work, an atlas-based statistical model for brain shift prediction, which accounts for uncertainty in the intraoperative environment, has been proposed. Previous work reported in the literature using this technique did not account for local deformation caused by surgical retraction. It is challenging to precisely localize the retractor location prior to surgery and the retractor is often moved in the course of the procedure. This paper proposes a technique that involves computing the retractor-induced brain deformation in the operating room through an active model solve and linearly superposing the solution with the precomputed deformation atlas. As a result, the new method takes advantage of the atlas-based framework’s accounting for uncertainties while also incorporating the effects of retraction with minimal intraoperative computing. This new approach was tested using simulation and phantom experiments. The results showed an improvement in average shift correction from 50% (ranging from 14 to 81%) for gravity atlas alone to 80% using the active solve retraction component (ranging from 73 to 85%). This paper presents a novel yet simple way to integrate retraction into the atlas-based brain shift computation framework. PMID:23864146

  8. Monitoring the injured brain: registered, patient specific atlas models to improve accuracy of recovered brain saturation values

    NASA Astrophysics Data System (ADS)

    Clancy, Michael; Belli, Antonio; Davies, David; Lucas, Samuel J. E.; Su, Zhangjie; Dehghani, Hamid

    2015-07-01

    The subject of superficial contamination and signal origins remains a widely debated topic in the field of Near Infrared Spectroscopy (NIRS), yet the concept of using the technology to monitor an injured brain, in a clinical setting, poses additional challenges concerning the quantitative accuracy of recovered parameters. Using high density diffuse optical tomography probes, quantitatively accurate parameters from different layers (skin, bone and brain) can be recovered from subject specific reconstruction models. This study assesses the use of registered atlas models for situations where subject specific models are not available. Data simulated from subject specific models were reconstructed using the 8 registered atlas models implementing a regional (layered) parameter recovery in NIRFAST. A 3-region recovery based on the atlas model yielded recovered brain saturation values which were accurate to within 4.6% (percentage error) of the simulated values, validating the technique. The recovered saturations in the superficial regions were not quantitatively accurate. These findings highlight differences in superficial (skin and bone) layer thickness between the subject and atlas models. This layer thickness mismatch was propagated through the reconstruction process decreasing the parameter accuracy.

  9. A Unified Framework for Cross-modality Multi-atlas Segmentation of Brain MRI

    PubMed Central

    Iglesias, Juan Eugenio; Sabuncu, Mert Rory; Leemput, Koen Van

    2013-01-01

    Multi-atlas label fusion is a powerful image segmentation strategy that is becoming increasingly popular in medical imaging. A standard label fusion algorithm relies on independently computed pairwise registrations between individual atlases and the (target) image to be segmented. These registrations are then used to propagate the atlas labels to the target space and fuse them into a single final segmentation. Such label fusion schemes commonly rely on the similarity between intensity values of the atlases and target scan, which is often problematic in medical imaging - in particular, when the atlases and target images are obtained via different sensor types or imaging protocols. In this paper, we present a generative probabilistic model that yields an algorithm for solving the atlas-to-target registrations and label fusion steps simultaneously. The proposed model does not directly rely on the similarity of image intensities. Instead, it exploits the consistency of voxel intensities within the target scan to drive the registration and label fusion, hence the atlases and target image can be of different modalities. Furthermore, the framework models the joint warp of all the atlases, introducing interdependence between the registrations. We use variational expectation maximization and the Demons registration framework in order to efficiently identify the most probable segmentation and registrations. We use two sets of experiments to illustrate the approach, where proton density (PD) MRI atlases are used to segment T1-weighted brain scans and vice versa. Our results clearly demonstrate the accuracy gain due to exploiting within-target intensity consistency and integrating registration into label fusion. PMID:24001931

  10. Spatial-temporal atlas of human fetal brain development during the early second trimester.

    PubMed

    Zhan, Jinfeng; Dinov, Ivo D; Li, Junning; Zhang, Zhonghe; Hobel, Sam; Shi, Yonggang; Lin, Xiangtao; Zamanyan, Alen; Feng, Lei; Teng, Gaojun; Fang, Fang; Tang, Yuchun; Zang, Fengchao; Toga, Arthur W; Liu, Shuwei

    2013-11-15

    During the second trimester, the human fetal brain undergoes numerous changes that lead to substantial variation in the neonatal in terms of its morphology and tissue types. As fetal MRI is more and more widely used for studying the human brain development during this period, a spatiotemporal atlas becomes necessary for characterizing the dynamic structural changes. In this study, 34 postmortem human fetal brains with gestational ages ranging from 15 to 22 weeks were scanned using 7.0 T MR. We used automated morphometrics, tensor-based morphometry and surface modeling techniques to analyze the data. Spatiotemporal atlases of each week and the overall atlas covering the whole period with high resolution and contrast were created. These atlases were used for the analysis of age-specific shape changes during this period, including development of the cerebral wall, lateral ventricles, Sylvian fissure, and growth direction based on local surface measurements. Our findings indicate that growth of the subplate zone is especially striking and is the main cause for the lamination pattern changes. Changes in the cortex around Sylvian fissure demonstrate that cortical growth may be one of the mechanisms for gyration. Surface deformation mapping, revealed by local shape analysis, indicates that there is global anterior-posterior growth pattern, with frontal and temporal lobes developing relatively quickly during this period. Our results are valuable for understanding the normal brain development trajectories and anatomical characteristics. These week-by-week fetal brain atlases can be used as reference in in vivo studies, and may facilitate the quantification of fetal brain development across space and time.

  11. The human brain in 1700 pieces: design and development of a three-dimensional, interactive and reference atlas.

    PubMed

    Nowinski, W L; Chua, B C; Qian, G Y; Nowinska, N G

    2012-02-15

    As the human brain is the most complex living organ, constructing its detailed model with exploration capabilities in a form of an atlas is a challenge. Our overall goal is to construct an advanced, detailed, parcellated, labeled, accurate, interactive, three-dimensional (3D), and scalable whole human brain atlas of structure, vasculature, tracts and systems. The objectives of this work are three-fold; to present: (1) method of atlas design and development including design principles, accuracy requirements, atlas content, architecture, functionality, user interface, and customized tools; (2) creation of an atlas of structure and systems including its modeling method and validation; and (3) integration of this atlas with the cerebrovasculature and tracts created earlier. The atlas is created from multiple in vivo 3/7 T scans. Its design based on "pyramidal principle" enables scalability while preserving design principles and exploits interaction paradigm "from blocks to brain". The atlas contains (1) navigator with modules for system/object/object state management, interaction, user interfacing, and rendering; and (2) brain model with cerebrum, cerebellum, brainstem, spinal cord, white matter, deep structures, systems, ventricles, arteries, veins, sinuses, and tracts. The brain model is parcellated, labeled, consistent, realistic, of high resolution, polygonal/volumetric, dissectible, extendable, and deformable. It has over 1700 3D components. The atlas has sub-voxel accuracy of 0.1mm and the smallest vessels of 80 μm. Brain exploration includes dynamic scene composition, manipulation-independent 3D labeling, interaction combined with animation, meta-labeling, and quantification. This atlas is useful in education, research, and clinical applications. It can potentially be foundation for a multi-level molecular-cellular-anatomical-physiological-behavioral platform. PMID:22062451

  12. Parcellation of the Healthy Neonatal Brain into 107 Regions Using Atlas Propagation through Intermediate Time Points in Childhood

    PubMed Central

    Blesa, Manuel; Serag, Ahmed; Wilkinson, Alastair G.; Anblagan, Devasuda; Telford, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Macnaught, Gillian; Semple, Scott I.; Bastin, Mark E.; Boardman, James P.

    2016-01-01

    Neuroimage analysis pipelines rely on parcellated atlases generated from healthy individuals to provide anatomic context to structural and diffusion MRI data. Atlases constructed using adult data introduce bias into studies of early brain development. We aimed to create a neonatal brain atlas of healthy subjects that can be applied to multi-modal MRI data. Structural and diffusion 3T MRI scans were acquired soon after birth from 33 typically developing neonates born at term (mean postmenstrual age at birth 39+5 weeks, range 37+2–41+6). An adult brain atlas (SRI24/TZO) was propagated to the neonatal data using temporal registration via childhood templates with dense temporal samples (NIH Pediatric Database), with the final atlas (Edinburgh Neonatal Atlas, ENA33) constructed using the Symmetric Group Normalization (SyGN) method. After this step, the computed final transformations were applied to T2-weighted data, and fractional anisotropy, mean diffusivity, and tissue segmentations to provide a multi-modal atlas with 107 anatomical regions; a symmetric version was also created to facilitate studies of laterality. Volumes of each region of interest were measured to provide reference data from normal subjects. Because this atlas is generated from step-wise propagation of adult labels through intermediate time points in childhood, it may serve as a useful starting point for modeling brain growth during development. PMID:27242423

  13. Parcellation of the Healthy Neonatal Brain into 107 Regions Using Atlas Propagation through Intermediate Time Points in Childhood.

    PubMed

    Blesa, Manuel; Serag, Ahmed; Wilkinson, Alastair G; Anblagan, Devasuda; Telford, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Macnaught, Gillian; Semple, Scott I; Bastin, Mark E; Boardman, James P

    2016-01-01

    Neuroimage analysis pipelines rely on parcellated atlases generated from healthy individuals to provide anatomic context to structural and diffusion MRI data. Atlases constructed using adult data introduce bias into studies of early brain development. We aimed to create a neonatal brain atlas of healthy subjects that can be applied to multi-modal MRI data. Structural and diffusion 3T MRI scans were acquired soon after birth from 33 typically developing neonates born at term (mean postmenstrual age at birth 39(+5) weeks, range 37(+2)-41(+6)). An adult brain atlas (SRI24/TZO) was propagated to the neonatal data using temporal registration via childhood templates with dense temporal samples (NIH Pediatric Database), with the final atlas (Edinburgh Neonatal Atlas, ENA33) constructed using the Symmetric Group Normalization (SyGN) method. After this step, the computed final transformations were applied to T2-weighted data, and fractional anisotropy, mean diffusivity, and tissue segmentations to provide a multi-modal atlas with 107 anatomical regions; a symmetric version was also created to facilitate studies of laterality. Volumes of each region of interest were measured to provide reference data from normal subjects. Because this atlas is generated from step-wise propagation of adult labels through intermediate time points in childhood, it may serve as a useful starting point for modeling brain growth during development.

  14. Development and validation of an atlas-based finite element brain model.

    PubMed

    Miller, Logan E; Urban, Jillian E; Stitzel, Joel D

    2016-10-01

    Traumatic brain injury is a leading cause of disability and injury-related death. To enhance our ability to prevent such injuries, brain response can be studied using validated finite element (FE) models. In the current study, a high-resolution, anatomically accurate FE model was developed from the International Consortium for Brain Mapping brain atlas. Due to wide variation in published brain material parameters, optimal brain properties were identified using a technique called Latin hypercube sampling, which optimized material properties against three experimental cadaver tests to achieve ideal biomechanics. Additionally, falx pretension and thickness were varied in a lateral impact variation. The atlas-based brain model (ABM) was subjected to the boundary conditions from three high-rate experimental cadaver tests with different material parameter combinations. Local displacements, determined experimentally using neutral density targets, were compared to displacements predicted by the ABM at the same locations. Error between the observed and predicted displacements was quantified using CORrelation and Analysis (CORA), an objective signal rating method that evaluates the correlation of two curves. An average CORA score was computed for each variation and maximized to identify the optimal combination of parameters. The strongest relationships between CORA and material parameters were observed for the shear parameters. Using properties obtained through the described multiobjective optimization, the ABM was validated in three impact configurations and shows good agreement with experimental data. The final model developed in this study consists of optimized brain material properties and was validated in three cadaver impacts against local brain displacement data.

  15. Development and validation of an atlas-based finite element brain model.

    PubMed

    Miller, Logan E; Urban, Jillian E; Stitzel, Joel D

    2016-10-01

    Traumatic brain injury is a leading cause of disability and injury-related death. To enhance our ability to prevent such injuries, brain response can be studied using validated finite element (FE) models. In the current study, a high-resolution, anatomically accurate FE model was developed from the International Consortium for Brain Mapping brain atlas. Due to wide variation in published brain material parameters, optimal brain properties were identified using a technique called Latin hypercube sampling, which optimized material properties against three experimental cadaver tests to achieve ideal biomechanics. Additionally, falx pretension and thickness were varied in a lateral impact variation. The atlas-based brain model (ABM) was subjected to the boundary conditions from three high-rate experimental cadaver tests with different material parameter combinations. Local displacements, determined experimentally using neutral density targets, were compared to displacements predicted by the ABM at the same locations. Error between the observed and predicted displacements was quantified using CORrelation and Analysis (CORA), an objective signal rating method that evaluates the correlation of two curves. An average CORA score was computed for each variation and maximized to identify the optimal combination of parameters. The strongest relationships between CORA and material parameters were observed for the shear parameters. Using properties obtained through the described multiobjective optimization, the ABM was validated in three impact configurations and shows good agreement with experimental data. The final model developed in this study consists of optimized brain material properties and was validated in three cadaver impacts against local brain displacement data. PMID:26762217

  16. A Probabilistic Atlas of Diffuse WHO Grade II Glioma Locations in the Brain

    PubMed Central

    Baumann, Cédric; Zouaoui, Sonia; Yordanova, Yordanka; Blonski, Marie; Rigau, Valérie; Chemouny, Stéphane; Taillandier, Luc; Bauchet, Luc; Duffau, Hugues; Paragios, Nikos

    2016-01-01

    Diffuse WHO grade II gliomas are diffusively infiltrative brain tumors characterized by an unavoidable anaplastic transformation. Their management is strongly dependent on their location in the brain due to interactions with functional regions and potential differences in molecular biology. In this paper, we present the construction of a probabilistic atlas mapping the preferential locations of diffuse WHO grade II gliomas in the brain. This is carried out through a sparse graph whose nodes correspond to clusters of tumors clustered together based on their spatial proximity. The interest of such an atlas is illustrated via two applications. The first one correlates tumor location with the patient’s age via a statistical analysis, highlighting the interest of the atlas for studying the origins and behavior of the tumors. The second exploits the fact that the tumors have preferential locations for automatic segmentation. Through a coupled decomposed Markov Random Field model, the atlas guides the segmentation process, and characterizes which preferential location the tumor belongs to and consequently which behavior it could be associated to. Leave-one-out cross validation experiments on a large database highlight the robustness of the graph, and yield promising segmentation results. PMID:26751577

  17. A Probabilistic Atlas of Diffuse WHO Grade II Glioma Locations in the Brain.

    PubMed

    Parisot, Sarah; Darlix, Amélie; Baumann, Cédric; Zouaoui, Sonia; Yordanova, Yordanka; Blonski, Marie; Rigau, Valérie; Chemouny, Stéphane; Taillandier, Luc; Bauchet, Luc; Duffau, Hugues; Paragios, Nikos

    2016-01-01

    Diffuse WHO grade II gliomas are diffusively infiltrative brain tumors characterized by an unavoidable anaplastic transformation. Their management is strongly dependent on their location in the brain due to interactions with functional regions and potential differences in molecular biology. In this paper, we present the construction of a probabilistic atlas mapping the preferential locations of diffuse WHO grade II gliomas in the brain. This is carried out through a sparse graph whose nodes correspond to clusters of tumors clustered together based on their spatial proximity. The interest of such an atlas is illustrated via two applications. The first one correlates tumor location with the patient's age via a statistical analysis, highlighting the interest of the atlas for studying the origins and behavior of the tumors. The second exploits the fact that the tumors have preferential locations for automatic segmentation. Through a coupled decomposed Markov Random Field model, the atlas guides the segmentation process, and characterizes which preferential location the tumor belongs to and consequently which behavior it could be associated to. Leave-one-out cross validation experiments on a large database highlight the robustness of the graph, and yield promising segmentation results.

  18. H. Julian Allen

    NASA Technical Reports Server (NTRS)

    1957-01-01

    H. Julian Allen stands beside the observation window of the 8 x 7 foot test section of the NACA Ames Unitary Plan Wind Tunnel. H. Julian Allen is best known for his 'Blunt Body Theory' of aerodynamics, a design technique for alleviating the severe re-entry heating problem which was then delaying the development of ballistic missiles. His findings revolutionized the fundamental design of ballistic missle re-entry shapes. Subsequently, applied research led to applications of the 'blunt' shape to ballistic missles and spacecraft which were intended to re-enter the Earth's atmosphere. This application led to the design of ablative heat shields that protected the Mercury, Gemini and Apollo astronauts as their space capsules re- entered the Earth's atmosphere. 'Harvey' Allen as he was called by most, was not only a brilliant scientist and aeronautical engineer but was also admired for his kindness, thoughtfulness and sense of humor. Among his many other accomplishments, Harvey Allen served as Center Director of the NASA Ames Research Center from 1965 to 1969. He died of a heart attack on January 29, 1977 at the age of 66.

  19. A review of Edward Flatau's 1894 Atlas of the Human Brain by the neurologist Sigmund Freud.

    PubMed

    Triarhou, Lazaros C

    2011-01-01

    In 1894, the Polish neurologist Edward Flatau (1868-1932), working in Berlin, published an exquisite photographic atlas of the unfixed human brain, preceding by 2 years Das Menschenhirn, the reference work of Gustaf Retzius (1842-1919) in Stockholm. In his early career as a neuroanatomist and neurologist, Sigmund Freud (1856-1939) wrote a review of Flatau's atlas for the Internationale klinische Rundschau, which has not been included in the 'Standard Edition of the Complete Psychological Works'. The aim of the present paper is twofold: to document Freud's review, and to revive the largely forgotten atlas of Flatau. The full text of Freud is presented in translation. Further, one element Flatau, Retzius and Freud had in common is discussed: their early role as protagonists and firm supporters of Ramón y Cajal's neuron theory, the cornerstone of modern neuroscience.

  20. Semi-Automated Atlas-based Analysis of Brain Histological Sections

    PubMed Central

    Kopec, Charles D.; Bowers, Amanda C.; Pai, Shraddha; Brody, Carlos D.

    2011-01-01

    Quantifying the location and/or number of features in a histological section of the brain currently requires one to first, manually register a corresponding section from a tissue atlas onto the experimental section and second, count the features. No automated method exists for the first process (registering), and most automated methods for the second process (feature counting) operate reliably only in a high signal-to-noise regime. To reduce experimenter bias and inconsistencies and increase the speed of these analyses, we developed Atlas Fitter, a semi-automated, open-source MatLab-based software package that assists in rapidly registering atlas panels onto histological sections. We also developed CellCounter, a novel fully-automated cell counting algorithm that is designed to operate on images with non-uniform background intensities and low signal-to-noise ratios. PMID:21194546

  1. Implementation of talairach atlas based automated brain segmentation for radiation therapy dosimetry.

    PubMed

    Popple, R A; Griffith, H R; Sawrie, S M; Fiveash, J B; Brezovich, I A

    2006-02-01

    Radiotherapy for brain cancer inevitably results in irradiation of uninvolved brain. While it has been demonstrated that irradiation of the brain can result in cognitive deficits, dose-volume relationships are not well established. There is little work correlating a particular cognitive deficit with dose received by the region of the brain responsible for the specific cognitive function. One obstacle to such studies is that identification of brain anatomy is both labor intensive and dependent on the individual performing the segmentation. Automatic segmentation has the potential to be both efficient and consistent. Brains2 is a software package developed by the University of Iowa for MRI volumetric studies. It utilizes MR images, the Talairach atlas, and an artificial neural network (ANN) to segment brain images into substructures in a standardized manner. We have developed a software package, Brains2DICOM, that converts the regions of interest identified by Brains2 into a DICOM radiotherapy structure set. The structure set can be imported into a treatment planning system for dosimetry. We demonstrated the utility of Brains2DICOM using a test case, a 34-year-old man with diffuse astrocytoma treated with three-dimensional conformal radiotherapy. Brains2 successfully applied the Talairach atlas to identify the right and left frontal, parietal, temporal, occipital, subcortical, and cerebellum regions. Brains2 was not successful in applying the ANN to identify small structures, such as the hippocampus and caudate. Further work is necessary to revise the ANN or to develop new methods for identification of small structures in the presence of disease and radiation induced changes. The segmented regions-of-interest were transferred to our commercial treatment planning system using DICOM and dose-volume histograms were constructed. This method will facilitate the acquisition of data necessary for the development of normal tissue complication probability (NTCP) models that

  2. The brain of the common vampire bat, Desmodus rotundus murinus (Wagner, 1840): a cytoarchitectural atlas.

    PubMed

    Bhatnagar, K P

    2008-08-01

    The vampire bat, Desmodus rotundus, is exceptionally agile and stealthy in nature. Feeding at night on cattle blood, it is a known scourge carrying rabies. It is endowed with a very high neocortical volume among bats, acute olfactory capabilities and an accessory olfactory system. These characteristics have resulted into an impressive number of neuroanatomical investigations except a long due atlas on its brain. This study presents a cytoarchitectural atlas of the brain of the common vampire, Desmodus rotundus murinus, in the frontal plane, serially between the olfactory bulb and the medulla oblongata. Twenty six selected sections are presented, each separated by about 300 to 560 microns. The atlas figures show lugol fast blue-cresyl echt violet stained hemisections with their matching half in a labeled line drawing. About 595 discrete brain structures (some repeating) have been identified. This study is likely to provide the accurate localization of nuclear groups, whole structures, fiber tracts, and interconnections to facilitate future neuroanatomical and neurophysiological investigations on the vampire brain.

  3. The brain of the common vampire bat, Desmodus rotundus murinus (Wagner, 1840): a cytoarchitectural atlas.

    PubMed

    Bhatnagar, K P

    2008-08-01

    The vampire bat, Desmodus rotundus, is exceptionally agile and stealthy in nature. Feeding at night on cattle blood, it is a known scourge carrying rabies. It is endowed with a very high neocortical volume among bats, acute olfactory capabilities and an accessory olfactory system. These characteristics have resulted into an impressive number of neuroanatomical investigations except a long due atlas on its brain. This study presents a cytoarchitectural atlas of the brain of the common vampire, Desmodus rotundus murinus, in the frontal plane, serially between the olfactory bulb and the medulla oblongata. Twenty six selected sections are presented, each separated by about 300 to 560 microns. The atlas figures show lugol fast blue-cresyl echt violet stained hemisections with their matching half in a labeled line drawing. About 595 discrete brain structures (some repeating) have been identified. This study is likely to provide the accurate localization of nuclear groups, whole structures, fiber tracts, and interconnections to facilitate future neuroanatomical and neurophysiological investigations on the vampire brain. PMID:18833481

  4. Workflow and atlas system for brain-wide mapping of axonal connectivity in rat.

    PubMed

    Zakiewicz, Izabela M; van Dongen, Yvette C; Leergaard, Trygve B; Bjaalie, Jan G

    2011-01-01

    Detailed knowledge about the anatomical organization of axonal connections is important for understanding normal functions of brain systems and disease-related dysfunctions. Such connectivity data are typically generated in neuroanatomical tract-tracing experiments in which specific axonal connections are visualized in histological sections. Since journal publications typically only accommodate restricted data descriptions and example images, literature search is a cumbersome way to retrieve overviews of brain connectivity. To explore more efficient ways of mapping, analyzing, and sharing detailed axonal connectivity data from the rodent brain, we have implemented a workflow for data production and developed an atlas system tailored for online presentation of axonal tracing data. The system is available online through the Rodent Brain WorkBench (www.rbwb.org; Whole Brain Connectivity Atlas) and holds experimental metadata and high-resolution images of histological sections from experiments in which axonal tracers were injected in the primary somatosensory cortex. We here present the workflow and the data system, and exemplify how the online image repository can be used to map different aspects of the brain-wide connectivity of the rat primary somatosensory cortex, including not only presence of connections but also morphology, densities, and spatial organization. The accuracy of the approach is validated by comparing results generated with our system with findings reported in previous publications. The present study is a contribution to a systematic mapping of rodent brain connections and represents a starting point for further large-scale mapping efforts.

  5. Workflow and atlas system for brain-wide mapping of axonal connectivity in rat.

    PubMed

    Zakiewicz, Izabela M; van Dongen, Yvette C; Leergaard, Trygve B; Bjaalie, Jan G

    2011-01-01

    Detailed knowledge about the anatomical organization of axonal connections is important for understanding normal functions of brain systems and disease-related dysfunctions. Such connectivity data are typically generated in neuroanatomical tract-tracing experiments in which specific axonal connections are visualized in histological sections. Since journal publications typically only accommodate restricted data descriptions and example images, literature search is a cumbersome way to retrieve overviews of brain connectivity. To explore more efficient ways of mapping, analyzing, and sharing detailed axonal connectivity data from the rodent brain, we have implemented a workflow for data production and developed an atlas system tailored for online presentation of axonal tracing data. The system is available online through the Rodent Brain WorkBench (www.rbwb.org; Whole Brain Connectivity Atlas) and holds experimental metadata and high-resolution images of histological sections from experiments in which axonal tracers were injected in the primary somatosensory cortex. We here present the workflow and the data system, and exemplify how the online image repository can be used to map different aspects of the brain-wide connectivity of the rat primary somatosensory cortex, including not only presence of connections but also morphology, densities, and spatial organization. The accuracy of the approach is validated by comparing results generated with our system with findings reported in previous publications. The present study is a contribution to a systematic mapping of rodent brain connections and represents a starting point for further large-scale mapping efforts. PMID:21829640

  6. Non-local Atlas-guided Multi-channel Forest Learning for Human Brain Labeling

    PubMed Central

    Ma, Guangkai; Gao, Yaozong; Wu, Guorong; Wu, Ligang; Shen, Dinggang

    2015-01-01

    Labeling MR brain images into anatomically meaningful regions is important in many quantitative brain researches. In many existing label fusion methods, appearance information is widely used. Meanwhile, recent progress in computer vision suggests that the context feature is very useful in identifying an object from a complex scene. In light of this, we propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). In particular, we employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and the target labels (i.e., corresponding to certain anatomical structures). Moreover, to accommodate the high inter-subject variations, we further extend our learning-based label fusion to a multi-atlas scenario, i.e., we train a random forest for each atlas and then obtain the final labeling result according to the consensus of all atlases. We have comprehensively evaluated our method on both LONI-LBPA40 and IXI datasets, and achieved the highest labeling accuracy, compared to the state-of-the-art methods in the literature. PMID:26942235

  7. A 3-dimensional digital atlas of the ascending sensory and the descending motor systems in the pigeon brain.

    PubMed

    Güntürkün, Onur; Verhoye, Marleen; De Groof, Geert; Van der Linden, Annemie

    2013-01-01

    Pigeons are classic animal models for learning, memory, and cognition. The majority of the current understanding about avian neurobiology outside of the domain of the song system has been established using pigeons. Since MRI represents an increasingly relevant tool for comparative neuroscience, a 3-dimensional MRI-based atlas of the pigeon brain becomes essential. Using multiple imaging protocols, we delineated diverse ascending sensory and descending motor systems as well as the hippocampal formation. This pigeon brain atlas can easily be used to determine the stereotactic location of identified neural structures at any angle of the head. In addition, the atlas is useful to find the optimal angle of sectioning for slice experiments, stereotactic injections and electrophysiological recordings. This pigeon brain atlas is freely available for the scientific community.

  8. The Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Deboer, David; Ackermann, Rob; Blitz, Leo; Bock, Douglas; Bower, Geoffrey; Davis, Michael; Dreher, John; Engargiola, Greg; Fleming, Matt; Keleta, Girmay; Harp, Gerry; Lugten, John; Tarter, Jill; Thornton, Doug; Wadefalk, Niklas; Weinreb, Sander; Welch, William J.

    2004-06-01

    The Allen Telescope Array, a joint project between the SETI Institute and the Radio Astronomy Laboratory at the University of California Berkeley, is currently under development and construction at the Hat Creek Radio Observatory in northern California. It will consist of 350 6.1-m offset Gregorian antennas in a fairly densely packed configuration, with minimum baselines of less than 10 m and a maximum baseline of about 900 m. The dual-polarization frequency range spans from about 500 MHz to 11 GHz, both polarizations of which are transported back from each antenna. The first generation processor will provide 32 synthesized beams of 104 MHz bandwidth, eight at each of four tunings, as well as outputs for a full-polarization correlator at two of the tunings at the same bandwidth. This paper provides a general description of the Allen Telescope Array.

  9. EPICS: Allen-Bradley hardware reference manual

    SciTech Connect

    Nawrocki, G.

    1993-04-05

    This manual covers the following hardware: Allen-Bradley 6008 -- SV VMEbus I/O scanner; Allen-Bradley universal I/O chassis 1771-A1B, -A2B, -A3B, and -A4B; Allen-Bradley power supply module 1771-P4S; Allen-Bradley 1771-ASB remote I/O adapter module; Allen-Bradley 1771-IFE analog input module; Allen-Bradley 1771-OFE analog output module; Allen-Bradley 1771-IG(D) TTL input module; Allen-Bradley 1771-OG(d) TTL output; Allen-Bradley 1771-IQ DC selectable input module; Allen-Bradley 1771-OW contact output module; Allen-Bradley 1771-IBD DC (10--30V) input module; Allen-Bradley 1771-OBD DC (10--60V) output module; Allen-Bradley 1771-IXE thermocouple/millivolt input module; and the Allen-Bradley 2705 RediPANEL push button module.

  10. A brain MRI atlas of the common squirrel monkey, Saimiri sciureus

    NASA Astrophysics Data System (ADS)

    Gao, Yurui; Schilling, Kurt G.; Khare, Shweta P.; Panda, Swetasudha; Choe, Ann S.; Stepniewska, Iwona; Li, Xia; Ding, Zhoahua; Anderson, Adam; Landman, Bennett A.

    2014-03-01

    The common squirrel monkey, Saimiri sciureus, is a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. It is one of the most commonly used South American primates in biomedical research. Unlike its Old World macaque cousins, no digital atlases have described the organization of the squirrel monkey brain. Here, we present a multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. In vivo MRI acquisitions include high resolution T2 structural imaging and low resolution diffusion tensor imaging. Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging. Cortical regions were manually annotated on the co-registered volumes based on published histological sections.

  11. A three-dimensional stereotaxic MRI brain atlas of the cichlid fish Oreochromis mossambicus.

    PubMed

    Simões, José M; Teles, Magda C; Oliveira, Rui F; Van der Linden, Annemie; Verhoye, Marleen

    2012-01-01

    The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system. PMID:22984463

  12. A Three-Dimensional Stereotaxic MRI Brain Atlas of the Cichlid Fish Oreochromis mossambicus

    PubMed Central

    Simões, José M.; Teles, Magda C.; Oliveira, Rui F.; Van der Linden, Annemie; Verhoye, Marleen

    2012-01-01

    The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system. PMID:22984463

  13. New experimental results in atlas-based brain morphometry

    NASA Astrophysics Data System (ADS)

    Gee, James C.; Fabella, Brian A.; Fernandes, Siddharth E.; Turetsky, Bruce I.; Gur, Ruben C.; Gur, Raquel E.

    1999-05-01

    In a previous meeting, we described a computational approach to MRI morphometry, in which a spatial warp mapping a reference or atlas image into anatomic alignment with the subject is first inferred. Shape differences with respect to the atlas are then studied by calculating the pointwise Jacobian determinant for the warp, which provides a measure of the change in differential volume about a point in the reference as it transforms to its corresponding position in the subject. In this paper, the method is used to analyze sex differences in the shape and size of the corpus callosum in an ongoing study of a large population of normal controls. The preliminary results of the current analysis support findings in the literature that have observed the splenium to be larger in females than in males.

  14. Implementation of nonlinear registration of brain atlas based on piecewise grid system

    NASA Astrophysics Data System (ADS)

    Liu, Rong; Gu, Lixu; Xu, Jianrong

    2007-12-01

    In this paper, a multi-step registration method of brain atlas and clinical Magnetic Resonance Imaging (MRI) data based on Thin-Plate Splines (TPS) and Piecewise Grid System (PGS) is presented. The method can help doctors to determine the corresponding anatomical structure between patient image and the brain atlas by piecewise nonlinear registration. Since doctors mostly pay attention to particular Region of Interest (ROI), and a global nonlinear registration is quite time-consuming which is not suitable for real-time clinical application, we propose a novel method to conduct linear registration in global area before nonlinear registration is performed in selected ROI. The homogenous feature points are defined to calculate the transform matrix between patient data and the brain atlas to conclude the mapping function. Finally, we integrate the proposed approach into an application of neurosurgical planning and guidance system which lends great efficiency in both neuro-anatomical education and guiding of neurosurgical operations. The experimental results reveal that the proposed approach can keep an average registration error of 0.25mm in near real-time manner.

  15. Hybrid atlas-based and image-based approach for segmenting 3D brain MRIs

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2001-07-01

    This work is a contribution to the problem of localizing key cerebral structures in 3D MRIs and its quantitative evaluation. In pursuing it, the cooperation between an image-based segmentation method and a hierarchical deformable registration approach has been considered. The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions of an image, I(s), from the data set are identified. These regions, M(I), are obtained combining information from deformable atlas, achieved by the warping of eight previous labeled maps on I(s). Then, the goal of the decision stage is to precisely locate the contours of the 3D regions set by the markers. This contour decision is performed by a 3D extension of the watershed transform. The anatomical structures taken into consideration and embedded into the atlas are brain, ventricles, corpus callosum, cerebellum, right and left hippocampus, medulla and midbrain. The hybrid method operates fully automatically and in 3D, successfully providing segmented brain structures. The quality of the segmentation has been studied in terms of the detected volume ratio by using kappa statistic and ROC analysis. Results of the method are shown and validated on a 3D MRI phantom. This study forms part of an on-going long term research aiming at the creation of a 3D probabilistic multi-purpose anatomical brain atlas.

  16. Integration of the Antennal Lobe Glomeruli and Three Projection Neurons in the Standard Brain Atlas of the Moth Heliothis Virescens

    PubMed Central

    Løfaldli, Bjarte Bye; Kvello, Pål; Mustaparta, Hanna

    2010-01-01

    Digital three dimensional standard brain atlases (SBAs) are valuable tools for integrating neuroimaging data of different preparations. In insects, SBAs of five species are available, including the atlas of the female Heliothis virescens moth brain. Like for the other species, the antennal lobes (ALs) of the moth brain atlas were integrated as one material identity without internal structures. Different from the others, the H. virescens SBA exclusively included the glomerular layer of the AL. This was an advantage in the present study for performing a direct registration of the glomerular layer of individual preparations into the standard brain. We here present the H. virescens female SBA with a new model of the AL glomeruli integrated into the atlas, i.e. with each of the 66 glomeruli identified and labelled with a specific number. The new model differs from the previous H. virescens AL model both in respect to the number of glomeruli and the numbering system; the latter according to the system used for the AL atlases of two other heliothine species. For identifying female specific glomeruli comparison with the male AL was necessary. This required a new male AL atlas, included in this paper. As demonstrated by the integration of three AL projection neurons of different preparations, the new SBA with the integrated glomruli is a helpful tool for determining the glomeruli innervated as well as the relative position of the axonal projections in the protocerebrum. PMID:20179785

  17. PCA and level set based non-rigid image registration for MRI and Paxinos-Watson atlas of rat brain

    NASA Astrophysics Data System (ADS)

    Cai, Chao; Liu, Ailing; Ding, Mingyue; Zhou, Chengping

    2007-12-01

    Image registration provides the ability to geometrically align one dataset with another. It is a basic task in a great variety of biomedical imaging applications. This paper introduced a novel three-dimensional registration method for Magnetic Resonance Image (MRI) and Paxinos-Watson Atlas of rat brain. For the purpose of adapting to a large range and non-linear deformation between MRI and atlas in higher registration accuracy, based on the segmentation of rat brain, we chose the principle components analysis (PCA) automatically performing the linear registration, and then, a level set based nonlinear registration correcting some small distortions. We implemented this registration method in a rat brain 3D reconstruction and analysis system. Experiments have demonstrated that this method can be successfully applied to registering the low resolution and noise affection MRI with Paxinos-Watson Atlas of rat brain.

  18. Combination strategies in multi-atlas image segmentation: application to brain MR data.

    PubMed

    Artaechevarria, Xabier; Munoz-Barrutia, Arrate; Ortiz-de-Solorzano, Carlos

    2009-08-01

    It has been shown that employing multiple atlas images improves segmentation accuracy in atlas-based medical image segmentation. Each atlas image is registered to the target image independently and the calculated transformation is applied to the segmentation of the atlas image to obtain a segmented version of the target image. Several independent candidate segmentations result from the process, which must be somehow combined into a single final segmentation. Majority voting is the generally used rule to fuse the segmentations, but more sophisticated methods have also been proposed. In this paper, we show that the use of global weights to ponderate candidate segmentations has a major limitation. As a means to improve segmentation accuracy, we propose the generalized local weighting voting method. Namely, the fusion weights adapt voxel-by-voxel according to a local estimation of segmentation performance. Using digital phantoms and MR images of the human brain, we demonstrate that the performance of each combination technique depends on the gray level contrast characteristics of the segmented region, and that no fusion method yields better results than the others for all the regions. In particular, we show that local combination strategies outperform global methods in segmenting high-contrast structures, while global techniques are less sensitive to noise when contrast between neighboring structures is low. We conclude that, in order to achieve the highest overall segmentation accuracy, the best combination method for each particular structure must be selected. PMID:19228554

  19. Automatic atlas-based volume estimation of human brain regions from MR images

    SciTech Connect

    Andreasen, N.C.; Rajarethinam, R.; Cizadlo, T.; Arndt, S.

    1996-01-01

    MRI offers many opportunities for noninvasive in vivo measurement of structure-function relationships in the human brain. Although automated methods are now available for whole-brain measurements, an efficient and valid automatic method for volume estimation of subregions such as the frontal or temporal lobes is still needed. We adapted the Talairach atlas to the study of brain subregions. We supplemented the atlas with additional boxes to include the cerebellum. We assigned all the boxes to 1 of 12 regions of interest (ROIs) (frontal, parietal, temporal, and occipital lobes, cerebellum, and subcortical regions on right and left sides of the brain).Using T1-weighted MR scans collected with an SPGR sequence (slice thickness = 1.5 mm), we manually traced these ROIs and produced volume estimates. We then transformed the scans into Talairach space and compared the volumes produced by the two methods ({open_quotes}traced{close_quotes} versus {open_quotes}automatic{close_quotes}). The traced measurements were considered to be the {open_quotes}gold standard{close_quotes} against which the automatic measurements were compared. The automatic method was found to produce measurements that were nearly identical to the traced method. We compared absolute measurements of volume produced by the two methods, as well as the sensitivity and specificity of the automatic method. We also compared the measurements of cerebral blood flow obtained through [{sup 15}O]H{sub 2}O PET studies in a sample of nine subjects. Absolute measurements of volume produced by the two methods were very similar, and the sensitivity and specificity of the automatic method were found to be high for all regions. The flow values were also found to be very similar by both methods. The automatic atlas-based method for measuring the volume of brain subregions produces results that are similar to manual techniques. 39 refs., 4 figs., 3 tabs.

  20. Multi-object model-based multi-atlas segmentation for rodent brains using dense discrete correspondences

    NASA Astrophysics Data System (ADS)

    Lee, Joohwi; Kim, Sun Hyung; Styner, Martin

    2016-03-01

    The delineation of rodent brain structures is challenging due to low-contrast multiple cortical and subcortical organs that are closely interfacing to each other. Atlas-based segmentation has been widely employed due to its ability to delineate multiple organs at the same time via image registration. The use of multiple atlases and subsequent label fusion techniques has further improved the robustness and accuracy of atlas-based segmentation. However, the accuracy of atlas-based segmentation is still prone to registration errors; for example, the segmentation of in vivo MR images can be less accurate and robust against image artifacts than the segmentation of post mortem images. In order to improve the accuracy and robustness of atlas-based segmentation, we propose a multi-object, model-based, multi-atlas segmentation method. We first establish spatial correspondences across atlases using a set of dense pseudo-landmark particles. We build a multi-object point distribution model using those particles in order to capture inter- and intra- subject variation among brain structures. The segmentation is obtained by fitting the model into a subject image, followed by label fusion process. Our result shows that the proposed method resulted in greater accuracy than comparable segmentation methods, including a widely used ANTs registration tool.

  1. Human Brain White Matter Atlas: Identification and Assignment of Common Anatomical Structures in Superficial White Matter

    PubMed Central

    Oishi, Kenichi; Zilles, Karl; Amunts, Katrin; Faria, Andreia; Jiang, Hangyi; Li, Xin; Akhter, Kazi; Hua, Kegang; Woods, Roger; Toga, Arthur W.; Pike, G. Bruce; Rosa-Neto, Pedro; Evans, Alan; Zhang, Jiangyang; Huang, Hao; Miller, Michael I.; van Zijl, Peter C.M.; Mazziotta, John; Mori, Susumu

    2008-01-01

    Structural delineation and assignment are the fundamental steps in understanding the anatomy of the human brain. The white matter has been structurally defined in the past only at its core regions (deep white matter). However, the most peripheral white matter areas, which are interleaved between the cortex and the deep white matter, have lacked clear anatomical definitions and parcellations. We used axonal fiber alignment information from diffusion tensor imaging (DTI) to delineate the peripheral white matter, and investigated its relationship with the cortex and the deep white matter. Using DTI data from 81 healthy subjects, we identified nine common, blade-like anatomical regions, which were further parcellated into 21 subregions based on the cortical anatomy. Four short association fiber tracts connecting adjacent gyri (U-fibers) were also identified reproducibly among the healthy population. We anticipate that this atlas will be useful resource for atlas-based white matter anatomical studies. PMID:18692144

  2. Digital, Three-dimensional Average Shaped Atlas of the Heliothis Virescens Brain with Integrated Gustatory and Olfactory Neurons

    PubMed Central

    Kvello, Pål; Løfaldli, Bjarte Bye; Rybak, Jürgen; Menzel, Randolf; Mustaparta, Hanna

    2009-01-01

    We use the moth Heliothis virescens as model organism for studying the neural network involved in chemosensory coding and learning. The constituent neurons are characterised by intracellular recordings combined with staining, resulting in a single neuron identified in each brain preparation. In order to spatially relate the neurons of different preparations a common brain framework was required. We here present an average shaped atlas of the moth brain. It is based on 11 female brain preparations, each stained with a fluorescent synaptic marker and scanned in confocal laser-scanning microscope. Brain neuropils of each preparation were manually reconstructed in the computer software Amira, followed by generating the atlas using the Iterative Shape Average Procedure. To demonstrate the application of the atlas we have registered two olfactory and two gustatory interneurons, as well as the axonal projections of gustatory receptor neurons into the atlas, visualising their spatial relationships. The olfactory interneurons, showing the typical morphology of inner-tract antennal lobe projection neurons, projected in the calyces of the mushroom body and laterally in the protocerebral lobe. The two gustatory interneurons, responding to sucrose and quinine respectively, projected in different areas of the brain. The wide projections of the quinine responding neuron included a lateral area adjacent to the projections of the olfactory interneurons. The sucrose responding neuron was confined to the suboesophageal ganglion with dendritic arborisations overlapping the axonal projections of the gustatory receptor neurons on the proboscis. By serving as a tool for the integration of neurons, the atlas offers visual access to the spatial relationship between the neurons in three dimensions, and thus facilitates the study of neuronal networks in the Heliothis virescens brain. The moth standard brain is accessible at http://www.ntnu.no/biolog/english/neuroscience/brain PMID:19949481

  3. Multidimensional MRI-CT atlas of the naked mole-rat brain (Heterocephalus glaber).

    PubMed

    Seki, Fumiko; Hikishima, Keigo; Nambu, Sanae; Okanoya, Kazuo; Okano, Hirotaka J; Sasaki, Erika; Miura, Kyoko; Okano, Hideyuki

    2013-01-01

    Naked mole-rats have a variety of distinctive features such as the organization of a hierarchical society (known as eusociality), extraordinary longevity, and cancer resistance; thus, it would be worthwhile investigating these animals in detail. One important task is the preparation of a brain atlas database that provide comprehensive information containing multidimensional data with various image contrasts, which can be achievable using a magnetic resonance imaging (MRI). Advanced MRI techniques such as diffusion tensor imaging (DTI), which generates high contrast images of fiber structures, can characterize unique morphological properties in addition to conventional MRI. To obtain high spatial resolution images, MR histology, DTI, and X-ray computed tomography were performed on the fixed adult brain. Skull and brain structures were segmented as well as reconstructed in stereotaxic coordinates. Data were also acquired for the neonatal brain to allow developmental changes to be observed. Moreover, in vivo imaging of naked mole-rats was established as an evaluation tool of live animals. The data obtained comprised three-dimensional (3D) images with high tissue contrast as well as stereotaxic coordinates. Developmental differences in the visual system were highlighted in particular by DTI. Although it was difficult to delineate optic nerves in the mature adult brain, parts of them could be distinguished in the immature neonatal brain. From observation of cortical thickness, possibility of high somatosensory system development replaced to the visual system was indicated. 3D visualization of brain structures in the atlas as well as the establishment of in vivo imaging would promote neuroimaging researches towards detection of novel characteristics of eusocial naked mole-rats. PMID:24391551

  4. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods.

    PubMed

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Wilkinson, A G; Macnaught, Gillian; Semple, Scott I; Boardman, James P

    2016-01-01

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases 'uniformly' distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course. PMID:27010238

  5. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods

    PubMed Central

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Wilkinson, A. G.; Macnaught, Gillian; Semple, Scott I.; Boardman, James P.

    2016-01-01

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases ‘uniformly’ distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course. PMID:27010238

  6. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods

    NASA Astrophysics Data System (ADS)

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Wilkinson, A. G.; MacNaught, Gillian; Semple, Scott I.; Boardman, James P.

    2016-03-01

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases ‘uniformly’ distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course.

  7. Nonlocal atlas-guided multi-channel forest learning for human brain labeling

    PubMed Central

    Ma, Guangkai; Gao, Yaozong; Wu, Guorong; Wu, Ligang; Shen, Dinggang

    2016-01-01

    Purpose: It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features can be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). Methods: In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. Results: The authors have comprehensively evaluated their method on both public LONI_LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the

  8. Three-dimensional average-shape atlas of the honeybee brain and its applications.

    PubMed

    Brandt, Robert; Rohlfing, Torsten; Rybak, Jürgen; Krofczik, Sabine; Maye, Alexander; Westerhoff, Malte; Hege, Hans-Christian; Menzel, Randolf

    2005-11-01

    The anatomical substrates of neural nets are usually composed from reconstructions of neurons that were stained in different preparations. Realistic models of the structural relationships between neurons require a common framework. Here we present 3-D reconstructions of single projection neurons (PN) connecting the antennal lobe (AL) with the mushroom body (MB) and lateral horn, groups of intrinsic mushroom body neurons (type 5 Kenyon cells), and a single mushroom body extrinsic neuron (PE1), aiming to compose components of the olfactory pathway in the honeybee. To do so, we constructed a digital standard atlas of the bee brain. The standard atlas was created as an average-shape atlas of 22 neuropils, calculated from 20 individual immunostained whole-mount bee brains. After correction for global size and positioning differences by repeatedly applying an intensity-based nonrigid registration algorithm, a sequence of average label images was created. The results were qualitatively evaluated by generating average gray-value images corresponding to the average label images and judging the level of detail within the labeled regions. We found that the first affine registration step in the sequence results in a blurred image because of considerable local shape differences. However, already the first nonrigid iteration in the sequence corrected for most of the shape differences among individuals, resulting in images rich in internal detail. A second iteration improved on that somewhat and was selected as the standard. Registering neurons from different preparations into the standard atlas reveals 1) that the m-ACT neuron occupies the entire glomerulus (cortex and core) and overlaps with a local interneuron in the cortical layer; 2) that, in the MB calyces and the lateral horn of the protocerebral lobe, the axon terminals of two identified m-ACT neurons arborize in separate but close areas of the neuropil; and 3) that MB-intrinsic clawed Kenyon cells (type 5), with somata

  9. Automatic macroscopic density artefact removal in a Nissl-stained microscopic atlas of whole mouse brain.

    PubMed

    Ding, W; Li, A; Wu, J; Yang, Z; Meng, Y; Wang, S; Gong, H

    2013-08-01

    Acquiring a whole mouse brain at the micrometer scale is a complex, continuous and time-consuming process. Because of defects caused by sample preparation and microscopy, the acquired image data sets suffer from various macroscopic density artefacts that worsen the image quality. We have to develop the available preprocessing methods to improve image quality by removing the artefacts that effect cell segmentation, vascular tracing and visualization. In this study, a set of automatic artefact removal methods is proposed for images obtained by tissue staining and optical microscopy. These methods significantly improve the complicated images that contain various structures, including cells and blood vessels. The whole mouse brain data set with Nissl staining was tested, and the intensity of the processed images was uniformly distributed throughout different brain areas. Furthermore, the processed image data set with its uniform brightness and high quality is now a fundamental atlas for image analysis, including cell segmentation, vascular tracing and visualization.

  10. A mesoscale connectome of the mouse brain.

    PubMed

    Oh, Seung Wook; Harris, Julie A; Ng, Lydia; Winslow, Brent; Cain, Nicholas; Mihalas, Stefan; Wang, Quanxin; Lau, Chris; Kuan, Leonard; Henry, Alex M; Mortrud, Marty T; Ouellette, Benjamin; Nguyen, Thuc Nghi; Sorensen, Staci A; Slaughterbeck, Clifford R; Wakeman, Wayne; Li, Yang; Feng, David; Ho, Anh; Nicholas, Eric; Hirokawa, Karla E; Bohn, Phillip; Joines, Kevin M; Peng, Hanchuan; Hawrylycz, Michael J; Phillips, John W; Hohmann, John G; Wohnoutka, Paul; Gerfen, Charles R; Koch, Christof; Bernard, Amy; Dang, Chinh; Jones, Allan R; Zeng, Hongkui

    2014-04-10

    Comprehensive knowledge of the brain's wiring diagram is fundamental for understanding how the nervous system processes information at both local and global scales. However, with the singular exception of the C. elegans microscale connectome, there are no complete connectivity data sets in other species. Here we report a brain-wide, cellular-level, mesoscale connectome for the mouse. The Allen Mouse Brain Connectivity Atlas uses enhanced green fluorescent protein (EGFP)-expressing adeno-associated viral vectors to trace axonal projections from defined regions and cell types, and high-throughput serial two-photon tomography to image the EGFP-labelled axons throughout the brain. This systematic and standardized approach allows spatial registration of individual experiments into a common three dimensional (3D) reference space, resulting in a whole-brain connectivity matrix. A computational model yields insights into connectional strength distribution, symmetry and other network properties. Virtual tractography illustrates 3D topography among interconnected regions. Cortico-thalamic pathway analysis demonstrates segregation and integration of parallel pathways. The Allen Mouse Brain Connectivity Atlas is a freely available, foundational resource for structural and functional investigations into the neural circuits that support behavioural and cognitive processes in health and disease. PMID:24695228

  11. Quantitative map of multiple auditory cortical regions with a stereotaxic fine-scale atlas of the mouse brain

    PubMed Central

    Tsukano, Hiroaki; Horie, Masao; Hishida, Ryuichi; Takahashi, Kuniyuki; Takebayashi, Hirohide; Shibuki, Katsuei

    2016-01-01

    Optical imaging studies have recently revealed the presence of multiple auditory cortical regions in the mouse brain. We have previously demonstrated, using flavoprotein fluorescence imaging, at least six regions in the mouse auditory cortex, including the anterior auditory field (AAF), primary auditory cortex (AI), the secondary auditory field (AII), dorsoanterior field (DA), dorsomedial field (DM), and dorsoposterior field (DP). While multiple regions in the visual cortex and somatosensory cortex have been annotated and consolidated in recent brain atlases, the multiple auditory cortical regions have not yet been presented from a coronal view. In the current study, we obtained regional coordinates of the six auditory cortical regions of the C57BL/6 mouse brain and illustrated these regions on template coronal brain slices. These results should reinforce the existing mouse brain atlases and support future studies in the auditory cortex. PMID:26924462

  12. A human brain atlas derived via n-cut parcellation of resting-state and task-based fMRI data.

    PubMed

    James, George Andrew; Hazaroglu, Onder; Bush, Keith A

    2016-02-01

    The growth of functional MRI has led to development of human brain atlases derived by parcellating resting-state connectivity patterns into functionally independent regions of interest (ROIs). All functional atlases to date have been derived from resting-state fMRI data. But given that functional connectivity between regions varies with task, we hypothesized that an atlas incorporating both resting-state and task-based fMRI data would produce an atlas with finer characterization of task-relevant regions than an atlas derived from resting-state alone. To test this hypothesis, we derived parcellation atlases from twenty-nine healthy adult participants enrolled in the Cognitive Connectome project, an initiative to improve functional MRI's translation into clinical decision-making by mapping normative variance in brain-behavior relationships. Participants underwent resting-state and task-based fMRI spanning nine cognitive domains: motor, visuospatial, attention, language, memory, affective processing, decision-making, working memory, and executive function. Spatially constrained n-cut parcellation derived brain atlases using (1) all participants' functional data (Task) or (2) a single resting-state scan (Rest). An atlas was also derived from random parcellation for comparison purposes (Random). Two methods were compared: (1) a parcellation applied to the group's mean edge weights (mean), and (2) a two-stage approach with parcellation of individual edge weights followed by parcellation of mean binarized edges (two-stage). The resulting Task and Rest atlases had significantly greater similarity with each other (mean Jaccard indices JI=0.72-0.85) than with the Random atlases (JI=0.59-0.63; all p<0.001 after Bonferroni correction). Task and Rest atlas similarity was greatest for the two-stage method (JI=0.85), which has been shown as more robust than the mean method; these atlases also better reproduced voxelwise seed maps of the left dorsolateral prefrontal cortex during

  13. Multi-Contrast Multi-Atlas Parcellation of Diffusion Tensor Imaging of the Human Brain

    PubMed Central

    Tang, Xiaoying; Yoshida, Shoko; Hsu, John; Huisman, Thierry A. G. M.; Faria, Andreia V.; Oishi, Kenichi; Kutten, Kwame; Poretti, Andrea; Li, Yue; Miller, Michael I.; Mori, Susumu

    2014-01-01

    In this paper, we propose a novel method for parcellating the human brain into 193 anatomical structures based on diffusion tensor images (DTIs). This was accomplished in the setting of multi-contrast diffeomorphic likelihood fusion using multiple DTI atlases. DTI images are modeled as high dimensional fields, with each voxel exhibiting a vector valued feature comprising of mean diffusivity (MD), fractional anisotropy (FA), and fiber angle. For each structure, the probability distribution of each element in the feature vector is modeled as a mixture of Gaussians, the parameters of which are estimated from the labeled atlases. The structure-specific feature vector is then used to parcellate the test image. For each atlas, a likelihood is iteratively computed based on the structure-specific vector feature. The likelihoods from multiple atlases are then fused. The updating and fusing of the likelihoods is achieved based on the expectation-maximization (EM) algorithm for maximum a posteriori (MAP) estimation problems. We first demonstrate the performance of the algorithm by examining the parcellation accuracy of 18 structures from 25 subjects with a varying degree of structural abnormality. Dice values ranging 0.8–0.9 were obtained. In addition, strong correlation was found between the volume size of the automated and the manual parcellation. Then, we present scan-rescan reproducibility based on another dataset of 16 DTI images – an average of 3.73%, 1.91%, and 1.79% for volume, mean FA, and mean MD respectively. Finally, the range of anatomical variability in the normal population was quantified for each structure. PMID:24809486

  14. Intramolecular ketene-allene cycloadditions.

    PubMed

    McCaleb, K L; Halcomb, R L

    2000-08-24

    [reaction: see text]This report describes intramolecular thermal [2 + 2] cycloadditions between ketenes and allenes. The formation of ketenes and the subsequent cycloadditions occurred under a variety of conditions, affording 7-methylidinebicyclo[3.2.0]heptanones and 7-methylidinebicyclo[3.1.1]heptanones in 45-78% yields. The regioselectivity of the cycloaddition varied with the substitution of the allene, and the yield of cyclized products varied with reaction conditions.

  15. Reconstruction of an arbitrary cross section from the serial drawings of a stereotaxic brain atlas.

    PubMed

    Suetens, P; Oosterlinck, A; Gybels, J

    1980-02-01

    A method is described for the reconstruction of arbitrary cross section from the serial line drawings of a stereotaxic brain atlas. Mathematically, the problem reduces to the intersection of a plane with a line pattern lying in another plane. However, the calculation yields a cloud of points, often confusing and unusable for the surgeon. Because it is impossible to link correctly all the calculated points in all cases [1,2], we propose a method where the number of points is drastically reduced: only regions of interest are depicted, i.e., the area where the electrode point is situated and the neighbouring regions. Instead of points, symbols are displayed, each symbol representing a different region. The efficiency of the method is shown using an atlas simulation of four intersecting spheres in the three dimensional space, Although the procedure is useful for all stereotaxic brain atlasses, a practical example is given where the poor quality of the reconstructed images does not allow good interpretation.

  16. Automatic Testing and Assessment of Neuroanatomy Using a Digital Brain Atlas: Method and Development of Computer- and Mobile-Based Applications

    ERIC Educational Resources Information Center

    Nowinski, Wieslaw L.; Thirunavuukarasuu, Arumugam; Ananthasubramaniam, Anand; Chua, Beng Choon; Qian, Guoyu; Nowinska, Natalia G.; Marchenko, Yevgen; Volkau, Ihar

    2009-01-01

    Preparation of tests and student's assessment by the instructor are time consuming. We address these two tasks in neuroanatomy education by employing a digital media application with a three-dimensional (3D), interactive, fully segmented, and labeled brain atlas. The anatomical and vascular models in the atlas are linked to "Terminologia…

  17. The Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    DeBoer, David R.; Welch, William J.; Dreher, John; Tarter, Jill; Blitz, Leo; Davis, Michael; Fleming, Matt; Bock, Douglas; Bower, Geoffrey; Lugten, John; Girmay-Keleta, G.; D'Addario, Larry R.; Harp, Gerry R.; Ackermann, Rob; Weinreb, Sander; Engargiola, Greg; Thornton, Doug; Wadefalk, Niklas

    2004-10-01

    The Allen Telescope Array, originally called the One Hectare Telescope (1hT) [1] will be a large array radio telescope whose novel characteristics will be a wide field of view (3.5 deg-GHz HPBW), continuous frequency coverage of 0.5 - 11 GHz, four dual-linear polarization output bands of 100 MHz each, four beams in each band, two 100 MHz spectral correlators for two of the bands, and hardware for RFI mitigation built in. Its scientific motivation is for deep SETI searches and, at the same time, a variety of other radio astronomy projects, including transient (e.g. pulsar) studies, HI mapping of the Milky Way and nearby galaxies, Zeeman studies of the galactic magnetic field in a number of transitions, mapping of long chain molecules in molecular clouds, mapping of the decrement in the cosmic background radiation toward galaxy clusters, and observation of HI absorption toward quasars at redshifts up to z=2. The array is planned for 350 6.1-meter dishes giving a physical collecting area of about 10,000 square meters. The large number of components reduces the price with economies of scale. The front end receiver is a single cryogenically cooled MIMIC Low Noise Amplifier covering the whole band. The feed is a wide-band log periodic feed of novel design, and the reflector system is an offset Gregorian for minimum sidelobes and spillover. All preliminary and critical design reviews have been completed. Three complete antennas with feeds and receivers are under test, and an array of 33 antennas is under construction at the Hat Creek Radio Observatory for the end of 2004. The present plan is to have a total of about 200 antennas completed by the summer of 2006 and the balance of the array finished before the end of the decade.

  18. Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Bower, Geoffrey

    2007-05-01

    The Allen Telescope Array (ATA) is a pioneering centimeter-wavelength radio telescope that will produce science that cannot be done with any other instrument. The ATA is the first radio telescope designed for commensal observing; it will undertake the most comprehensive and sensitive SETI surveys ever done as well as the deepest and largest area continuum and spectroscopic surveys. Science operations will commence this year with a 42-element array. The ATA will ultimately comprise 350 6-meter dishes at Hat Creek in California, and will make possible large, deep radio surveys that were not previously feasible. The telescope incorporates many new design features including hydroformed antenna surfaces, a log-periodic feed covering the entire range of frequencies from 500 MHz to 11.2 GHz, low noise, wide-band amplifiers with a flat response over the entire band. The full array has the sensitivity of the Very Large Array but with a survey capability that is greater by an order of magnitude due to the wide field of view of the 6-meter dishes. Even with 42 elements, the ATA will be one of the most powerful radio survey telescopes. Science goals include the Five GHz sky survey (FiGSS) to match the 1.4-GHz NRAO VLA Sky Survey (NVSS) and the Sloan Digital Sky Survey within the first year of operation with the 42 element array, and a deep all-sky survey of extragalactic hydrogen to investigate galaxy evolution and intergalactic gas accretion. Transient and variable source surveys, pulsar science, spectroscopy of new molecular species in the galaxy, large-scale mapping of galactic magnetic filaments, and wide-field imaging of comets and other solar system objects are among the other key science objectives of the ATA. SETI surveys will reach sufficient sensitivity to detect an Arecibo planetary radar from 1,000,000 stars to distances of 300 pc.

  19. A histology-based atlas of the C57BL/6J mouse brain deformably registered to in vivo MRI for localized radiation and surgical targeting

    NASA Astrophysics Data System (ADS)

    Purger, David; McNutt, Todd; Achanta, Pragathi; Quiñones-Hinojosa, Alfredo; Wong, John; Ford, Eric

    2009-12-01

    The C57BL/6J laboratory mouse is commonly used in neurobiological research. Digital atlases of the C57BL/6J brain have been used for visualization, genetic phenotyping and morphometry, but currently lack the ability to accurately calculate deviations between individual mice. We developed a fully three-dimensional digital atlas of the C57BL/6J brain based on the histology atlas of Paxinos and Franklin (2001 The Mouse Brain in Stereotaxic Coordinates 2nd edn (San Diego, CA: Academic)). The atlas uses triangular meshes to represent the various structures. The atlas structures can be overlaid and deformed to individual mouse MR images. For this study, we selected 18 structures from the histological atlas. Average atlases can be created for any group of mice of interest by calculating the mean three-dimensional positions of corresponding individual mesh vertices. As a validation of the atlas' accuracy, we performed deformable registration of the lateral ventricles to 13 MR brain scans of mice in three age groups: 5, 8 and 9 weeks old. Lateral ventricle structures from individual mice were compared to the corresponding average structures and the original histology structures. We found that the average structures created using our method more accurately represent individual anatomy than histology-based atlases alone, with mean vertex deviations of 0.044 mm versus 0.082 mm for the left lateral ventricle and 0.045 mm versus 0.068 mm for the right lateral ventricle. Our atlas representation gives direct spatial deviations for structures of interest. Our results indicate that MR-deformable histology-based atlases represent an accurate method to obtain accurate morphometric measurements of a population of mice, and that this method may be applied to phenotyping experiments in the future as well as precision targeting of surgical procedures or radiation treatment.

  20. A pre-computed brain response atlas for instantaneous strain estimation in contact sports

    PubMed Central

    Ji, Songbai; Zhao, Wei

    2014-01-01

    Finite element models of the human head play an important role in investigating the mechanisms of traumatic brain injury, including sports concussion. A critical limitation, however, is that they incur a substantial computational cost to simulate even a single impact. Therefore, current simulation schemes significantly hamper brain injury studies based on model-estimated tissue-level responses. In this study, we investigate the feasibility of a pre-computed brain response atlas (pcBRA) to substantially increase the simulation efficiency in estimating brain strains using isolated rotational acceleration impulses parameterized with four independent variables (peak magnitude and duration, and rotational axis azimuth and elevation angles) with values determined from on-field measurements. Using randomly generated testing datasets, the partially established pcBRA achieved a 100% success rate in interpolation based on element-wise differences in accumulated peak strain (εp) according to a “double-10%” criterion or average regional εp in generic regions and the corpus callosum. A similar performance was maintained in extrapolation. The pcBRA performance was further successfully evaluated against responses directly simulating two independently measured typical real-world rotational profiles. The computational cost to estimate element-wise whole-brain or regional εp was 6 sec and <0.01 sec, respectively, vs. ~50 min directly simulating a 40 ms impulse. These findings suggest the pcBRA could substantially increase the throughput in impact simulation without significant loss of accuracy from the estimation itself and, thus, its potential to accelerate the exploration of the mechanisms of sports concussion in general. If successful, the pcBRA may also become a diagnostic adjunct in conjunction with sensors that measure head impact kinematics on the field to objectively monitor and identify tissue-level brain trauma in real-time for “return-to-play” decision

  1. Multi-region labeling and segmentation using a graph topology prior and atlas information in brain images.

    PubMed

    Al-Shaikhli, Saif Dawood Salman; Yang, Michael Ying; Rosenhahn, Bodo

    2014-12-01

    Medical image segmentation and anatomical structure labeling according to the types of the tissues are important for accurate diagnosis and therapy. In this paper, we propose a novel approach for multi-region labeling and segmentation, which is based on a topological graph prior and the topological information of an atlas, using a modified multi-level set energy minimization method in brain images. We consider a topological graph prior and atlas information to evolve the contour based on a topological relationship presented via a graph relation. This novel method is capable of segmenting adjacent objects with very close gray level in low resolution brain image that would be difficult to segment correctly using standard methods. The topological information of an atlas are transformed to the topological graph of a low resolution (noisy) brain image to obtain region labeling. We explain our algorithm and show the topological graph prior and label transformation techniques to explain how it gives precise multi-region segmentation and labeling. The proposed algorithm is capable of segmenting and labeling different regions in noisy or low resolution MRI brain images of different modalities. We compare our approaches with other state-of-the-art approaches for multi-region labeling and segmentation.

  2. A Critique of Mark D. Allen's "The Preservation of Verb Subcategory Knowledge in a Spoken Language Comprehension Deficit"

    ERIC Educational Resources Information Center

    Kemmerer, David

    2008-01-01

    Allen [Allen, M. (2005). "The preservation of verb subcategory knowledge in a spoken language comprehension deficit." "Brain and Language, 95", 255-264.] reports a single patient, WBN, who, during spoken language comprehension, is still able to access some of the syntactic properties of verbs despite being unable to access some of their semantic…

  3. Statistical model of laminar structure for atlas-based segmentation of the fetal brain from in utero MR images

    NASA Astrophysics Data System (ADS)

    Habas, Piotr A.; Kim, Kio; Chandramohan, Dharshan; Rousseau, Francois; Glenn, Orit A.; Studholme, Colin

    2009-02-01

    Recent advances in MR and image analysis allow for reconstruction of high-resolution 3D images from clinical in utero scans of the human fetal brain. Automated segmentation of tissue types from MR images (MRI) is a key step in the quantitative analysis of brain development. Conventional atlas-based methods for adult brain segmentation are limited in their ability to accurately delineate complex structures of developing tissues from fetal MRI. In this paper, we formulate a novel geometric representation of the fetal brain aimed at capturing the laminar structure of developing anatomy. The proposed model uses a depth-based encoding of tissue occurrence within the fetal brain and provides an additional anatomical constraint in a form of a laminar prior that can be incorporated into conventional atlas-based EM segmentation. Validation experiments are performed using clinical in utero scans of 5 fetal subjects at gestational ages ranging from 20.5 to 22.5 weeks. Experimental results are evaluated against reference manual segmentations and quantified in terms of Dice similarity coefficient (DSC). The study demonstrates that the use of laminar depth-encoded tissue priors improves both the overall accuracy and precision of fetal brain segmentation. Particular refinement is observed in regions of the parietal and occipital lobes where the DSC index is improved from 0.81 to 0.82 for cortical grey matter, from 0.71 to 0.73 for the germinal matrix, and from 0.81 to 0.87 for white matter.

  4. Atlas-based segmentation of brain tumor images using a Markov random field-based tumor growth model and non-rigid registration.

    PubMed

    Bauer, Stefan; Seiler, Christof; Bardyn, Thibaut; Buechler, Philippe; Reyes, Mauricio

    2010-01-01

    We propose a new and clinically oriented approach to perform atlas-based segmentation of brain tumor images. A mesh-free method is used to model tumor-induced soft tissue deformations in a healthy brain atlas image with subsequent registration of the modified atlas to a pathologic patient image. The atlas is seeded with a tumor position prior and tumor growth simulating the tumor mass effect is performed with the aim of improving the registration accuracy in case of patients with space-occupying lesions. We perform tests on 2D axial slices of five different patient data sets and show that the approach gives good results for the segmentation of white matter, grey matter, cerebrospinal fluid and the tumor.

  5. Improving the quantitative accuracy of cerebral oxygen saturation in monitoring the injured brain using atlas based Near Infrared Spectroscopy models.

    PubMed

    Clancy, Michael; Belli, Antonio; Davies, David; Lucas, Samuel J E; Su, Zhangjie; Dehghani, Hamid

    2016-08-01

    The application of Near Infrared Spectroscopy (NIRS) for the monitoring of the cerebral oxygen saturation within the brain is well established, albeit using temporal data that can only measure relative changes of oxygenation state of the brain from a baseline. The focus of this investigation is to demonstrate that hybridisation of existing near infrared probe designs and reconstruction techniques can pave the way to produce a system and methods that can be used to monitor the absolute oxygen saturation in the injured brain. Using registered Atlas models in simulation, a novel method is outlined by which the quantitative accuracy and practicality of NIRS for specific use in monitoring the injured brain, can be improved, with cerebral saturation being recovered to within 10.1 ± 1.8% of the expected values. PMID:27003677

  6. Recent Advances in the Reactions of 1,2-Allenic Ketones and α-Allenic Alcohols.

    PubMed

    Fan, Xuesen; He, Yan; Zhang, Xinying

    2016-06-01

    This Personal Account summarizes our recent efforts in searching for novel synthetic strategies for a number of organic molecules by using allene derivatives as valuable substrates. It starts with a concise description of the background of allene-related synthetic chemistry. The second part deals with the reactions of 1,2-allenic ketones, including the reactions of 1,2-allenic ketones with various nucleophiles to afford functionalized benzenes, heterocycles, and fluoroenones, and those of allenic ketones as nucleophiles under the promotion of bases to provide 1,3,4'-triones or functionalized furans. The third part of this account focuses on the reactions of α-allenic alcohols. In this section, multicomponent reactions involving α-allenic alcohols, and cascade reactions of α-allenic alcohols promoted by Brønsted acid or iodine, are presented. PMID:27230525

  7. Waxholm Space atlas of the rat brain hippocampal region: three-dimensional delineations based on magnetic resonance and diffusion tensor imaging.

    PubMed

    Kjonigsen, Lisa J; Lillehaug, Sveinung; Bjaalie, Jan G; Witter, Menno P; Leergaard, Trygve B

    2015-03-01

    Atlases of the rat brain are widely used as reference for orientation, planning of experiments, and as tools for assigning location to experimental data. Improved quality and use of magnetic resonance imaging (MRI) and other tomographical imaging techniques in rats have allowed the development of new three-dimensional (3-D) volumetric brain atlas templates. The rat hippocampal region is a commonly used model for basic research on memory and learning, and for preclinical investigations of brain disease. The region features a complex anatomical organization with multiple subdivisions that can be identified on the basis of specific cytoarchitectonic or chemoarchitectonic criteria. We here investigate the extent to which it is possible to identify boundaries of divisions of the hippocampal region on the basis of high-resolution MRI contrast. We present the boundaries of 13 divisions, identified and delineated based on multiple types of image contrast observed in the recently published Waxholm Space MRI/DTI template for the Sprague Dawley rat brain (Papp et al., Neuroimage 97:374-386, 2014). The new detailed delineations of the hippocampal formation and parahippocampal region (Waxholm Space atlas of the Sprague Dawley rat brain, v2.0) are shared via the INCF Software Center (http://software.incf.org/), where also the MRI/DTI reference template is available. The present update of the Waxholm Space atlas of the rat brain is intended to facilitate interpretation, analysis, and integration of experimental data from this anatomically complex region.

  8. Stereoscopic three-dimensional visualization applied to multimodal brain images: clinical applications and a functional connectivity atlas

    PubMed Central

    Rojas, Gonzalo M.; Gálvez, Marcelo; Vega Potler, Natan; Craddock, R. Cameron; Margulies, Daniel S.; Castellanos, F. Xavier; Milham, Michael P.

    2014-01-01

    Effective visualization is central to the exploration and comprehension of brain imaging data. While MRI data are acquired in three-dimensional space, the methods for visualizing such data have rarely taken advantage of three-dimensional stereoscopic technologies. We present here results of stereoscopic visualization of clinical data, as well as an atlas of whole-brain functional connectivity. In comparison with traditional 3D rendering techniques, we demonstrate the utility of stereoscopic visualizations to provide an intuitive description of the exact location and the relative sizes of various brain landmarks, structures and lesions. In the case of resting state fMRI, stereoscopic 3D visualization facilitated comprehension of the anatomical position of complex large-scale functional connectivity patterns. Overall, stereoscopic visualization improves the intuitive visual comprehension of image contents, and brings increased dimensionality to visualization of traditional MRI data, as well as patterns of functional connectivity. PMID:25414626

  9. Stereoscopic three-dimensional visualization applied to multimodal brain images: clinical applications and a functional connectivity atlas.

    PubMed

    Rojas, Gonzalo M; Gálvez, Marcelo; Vega Potler, Natan; Craddock, R Cameron; Margulies, Daniel S; Castellanos, F Xavier; Milham, Michael P

    2014-01-01

    Effective visualization is central to the exploration and comprehension of brain imaging data. While MRI data are acquired in three-dimensional space, the methods for visualizing such data have rarely taken advantage of three-dimensional stereoscopic technologies. We present here results of stereoscopic visualization of clinical data, as well as an atlas of whole-brain functional connectivity. In comparison with traditional 3D rendering techniques, we demonstrate the utility of stereoscopic visualizations to provide an intuitive description of the exact location and the relative sizes of various brain landmarks, structures and lesions. In the case of resting state fMRI, stereoscopic 3D visualization facilitated comprehension of the anatomical position of complex large-scale functional connectivity patterns. Overall, stereoscopic visualization improves the intuitive visual comprehension of image contents, and brings increased dimensionality to visualization of traditional MRI data, as well as patterns of functional connectivity.

  10. A Digital Atlas of Middle to Large Brain Vessels and Their Relation to Cortical and Subcortical Structures

    PubMed Central

    Viviani, Roberto

    2016-01-01

    While widely distributed, the vascular supply of the brain is particularly prominent in certain anatomical structures because of the high vessel density or their large size. A digital atlas of middle to large vessels in Montreal Neurological Institute (MNI) coordinates is here presented, obtained from a sample of N = 38 healthy participants scanned with the time-of-flight (TOF) magnetic resonance technique, and normalized with procedures analogous to those commonly used in functional neuroimaging studies. Spatial colocalization of brain parenchyma and vessels is shown to affect specific structures such as the anteromedial face of the temporal lobe, the cortex surrounding the Sylvian fissure (Sy), the anterior cingular cortex, and the ventral striatum. The vascular frequency maps presented here provide objective information about the vascularization of the brain, and may assist in the interpretation of data in studies where vessels are a potential confound. PMID:26924965

  11. Water resources of Allen Parish

    USGS Publications Warehouse

    Prakken, Lawrence B.; Griffith, Jason M.; Fendick, Robert B.

    2012-01-01

    In 2005, approximately 29.2 million gallons per day (Mgal/d) of water were withdrawn in Allen Parish, Louisiana, including about 26.8 Mgal/d from groundwater sources and 2.45 Mgal/d from surface-water sources. Rice irrigation accounted for 74 percent (21.7 Mgal/d) of the total water withdrawn. Other categories of use included public supply, industrial, rural domestic, livestock, general irrigation, and aquaculture. Water-use data collected at 5-year intervals from 1960 to 2005 indicate water withdrawals in the parish were greatest in 1960 (119 Mgal/d) and 1980 (98.7 Mgal/d). The substantial decrease in surface-water use between 1960 and 1965 is primarily attributable to rice-irrigation withdrawals declining from 61.2 to 6.74 Mgal/d. This fact sheet summarizes information on the water resources of Allen Parish, La. Information on groundwater and surface-water availability, quality, development, use, and trends is based on previously published reports listed in the Selected References section.

  12. Gene expression based mouse brain parcellation using Markov random field regularized non-negative matrix factorization

    NASA Astrophysics Data System (ADS)

    Pathak, Sayan D.; Haynor, David R.; Thompson, Carol L.; Lein, Ed; Hawrylycz, Michael

    2009-02-01

    Understanding the geography of genetic expression in the mouse brain has opened previously unexplored avenues in neuroinformatics. The Allen Brain Atlas (www.brain-map.org) (ABA) provides genome-wide colorimetric in situ hybridization (ISH) gene expression images at high spatial resolution, all mapped to a common three-dimensional 200μm3 spatial framework defined by the Allen Reference Atlas (ARA) and is a unique data set for studying expression based structural and functional organization of the brain. The goal of this study was to facilitate an unbiased data-driven structural partitioning of the major structures in the mouse brain. We have developed an algorithm that uses nonnegative matrix factorization (NMF) to perform parts based analysis of ISH gene expression images. The standard NMF approach and its variants are limited in their ability to flexibly integrate prior knowledge, in the context of spatial data. In this paper, we introduce spatial connectivity as an additional regularization in NMF decomposition via the use of Markov Random Fields (mNMF). The mNMF algorithm alternates neighborhood updates with iterations of the standard NMF algorithm to exploit spatial correlations in the data. We present the algorithm and show the sub-divisions of hippocampus and somatosensory-cortex obtained via this approach. The results are compared with established neuroanatomic knowledge. We also highlight novel gene expression based sub divisions of the hippocampus identified by using the mNMF algorithm.

  13. Trans-cranial opening of the blood-brain barrier in targeted regions using a stereotaxic brain atlas and focused ultrasound energy

    PubMed Central

    2014-01-01

    Objective The blood-brain barrier (BBB) protects the brain by preventing the entry of large molecules; this poses a major obstacle for the delivery of drugs to the brain. A novel technique using focused ultrasound (FUS) energy combined with microbubble contrast agents has been widely used for non-invasive trans-cranial BBB opening. Traditionally, FUS research is conducted with magnetic resonance imaging (MRI) guidance, which is expensive and poses physical limitations due to the magnetic field. A system that could allow researchers to test brain therapies without MR intervention could facilitate and accelerate translational research. Methods In this study, we present a novel FUS system that uses a custom-built FUS generator mounted on a motorized stereotaxic apparatus with embedded brain atlas to locally open the BBB in rodents. The system was initially characterized using a tissue-mimicking phantom. Rodent studies were also performed to evaluate whether non-invasive, localized BBB opening could be achieved using brain atlas-based targeting. Brains were exposed to pulsed focused ultrasound energy at 1.06 MHz in rats and 3.23 MHz in mice, with the focal pressure estimated to be 0.5–0.6 MPa through the skull. BBB opening was confirmed in gross tissue sections by the presence of Evans blue leakage in the exposed region of the brain and by histological assessment. Results The targeting accuracy of the stereotaxic system was better than 0.5 mm in the tissue-mimicking phantom. Reproducible localized BBB opening was verified with Evans blue dye leakage in 32/33 rats and had a targeting accuracy of ±0.3 mm. The use of higher frequency exposures in mice enabled a similar precision of localized BBB opening as was observed with the low frequency in the rat model. Conclusions With this dedicated small-animal motorized stereotaxic-FUS system, we achieved accurate targeting of focused ultrasound exposures in the brain for non-invasive opening of the BBB. This system can

  14. Mapping heritability and molecular genetic associations with cortical features using probabilistic brain atlases: methods and applications to schizophrenia.

    PubMed

    Cannon, Tyrone D; Thompson, Paul M; van Erp, Theo G M; Huttunen, Matti; Lonnqvist, Jouko; Kaprio, Jaakko; Toga, Arthur W

    2006-01-01

    There is an urgent need to decipher the complex nature of genotype-phenotype relationships within the multiple dimensions of brain structure and function that are compromised in neuropsychiatric syndromes such as schizophrenia. Doing so requires sophisticated methodologies to represent population variability in neural traits and to probe their heritable and molecular genetic bases. We have recently developed and applied computational algorithms to map the heritability of, as well as genetic linkage and association to, neural features encoded using brain imaging in the context of three-dimensional (3D), populationbased, statistical brain atlases. One set of algorithms builds on our prior work using classical twin study methods to estimate heritability by fitting biometrical models for additive genetic, unique, and common environmental influences. Another set of algorithms performs regression-based (Haseman-Elston) identical-bydescent linkage analysis and genetic association analysis of DNA polymorphisms in relation to neural traits of interest in the same 3D population-based brain atlas format. We demonstrate these approaches using samples of healthy monozygotic (MZ) and dizygotic (DZ) twin pairs, as well as MZ and DZ twin pairs discordant for schizophrenia, but the methods can be generalized to other classes of relatives and to other diseases. The results confirm prior evidence of genetic influences on gray matter density in frontal brain regions. They also provide converging evidence that the chromosome 1q42 region is relevant to schizophrenia by demonstrating linkage and association of markers of the Transelin-Associated-Factor-X and Disrupted-In- Schizophrenia-1 genes with prefrontal cortical gray matter deficits in twins discordant for schizophrenia. PMID:16595856

  15. Automated tissue classification of pediatric brains from magnetic resonance images using age-specific atlases

    NASA Astrophysics Data System (ADS)

    Metzger, Andrew; Benavides, Amanda; Nopoulos, Peg; Magnotta, Vincent

    2016-03-01

    The goal of this project was to develop two age appropriate atlases (neonatal and one year old) that account for the rapid growth and maturational changes that occur during early development. Tissue maps from this age group were initially created by manually correcting the resulting tissue maps after applying an expectation maximization (EM) algorithm and an adult atlas to pediatric subjects. The EM algorithm classified each voxel into one of ten possible tissue types including several subcortical structures. This was followed by a novel level set segmentation designed to improve differentiation between distal cortical gray matter and white matter. To minimize the req uired manual corrections, the adult atlas was registered to the pediatric scans using high -dimensional, symmetric image normalization (SyN) registration. The subject images were then mapped to an age specific atlas space, again using SyN registration, and the resulting transformation applied to the manually corrected tissue maps. The individual maps were averaged in the age specific atlas space and blurred to generate the age appropriate anatomical priors. The resulting anatomical priors were then used by the EM algorithm to re-segment the initial training set as well as an independent testing set. The results from the adult and age-specific anatomical priors were compared to the manually corrected results. The age appropriate atlas provided superior results as compared to the adult atlas. The image analysis pipeline used in this work was built using the open source software package BRAINSTools.

  16. Individual 3D region-of-interest atlas of the human brain: knowledge-based class image analysis for extraction of anatomical objects

    NASA Astrophysics Data System (ADS)

    Wagenknecht, Gudrun; Kaiser, Hans-Juergen; Sabri, Osama; Buell, Udalrich

    2000-06-01

    After neural network-based classification of tissue types, the second step of atlas extraction is knowledge-based class image analysis to get anatomically meaningful objects. Basic algorithms are region growing, mathematical morphology operations, and template matching. A special algorithm was designed for each object. The class label of each voxel and the knowledge about the relative position of anatomical objects to each other and to the sagittal midplane of the brain can be utilized for object extraction. User interaction is only necessary to define starting, mid- and end planes for most object extractions and to determine the number of iterations for erosion and dilation operations. Extraction can be done for the following anatomical brain regions: cerebrum; cerebral hemispheres; cerebellum; brain stem; white matter (e.g., centrum semiovale); gray matter [cortex, frontal, parietal, occipital, temporal lobes, cingulum, insula, basal ganglia (nuclei caudati, putamen, thalami)]. For atlas- based quantification of functional data, anatomical objects can be convoluted with the point spread function of functional data to take into account the different resolutions of morphological and functional modalities. This method allows individual atlas extraction from MRI image data of a patient without the need of warping individual data to an anatomical or statistical MRI brain atlas.

  17. Reply to David Kemmerer's "A Critique of Mark D. Allen's "The Preservation of Verb Subcategory Knowledge in a Spoken Language Comprehension Deficit""

    ERIC Educational Resources Information Center

    Allen, Mark D.; Owens, Tyler E.

    2008-01-01

    Allen [Allen, M. D. (2005). The preservation of verb subcategory knowledge in a spoken language comprehension deficit. "Brain and Language, "95, 255-264] presents evidence from a single patient, WBN, to motivate a theory of lexical processing and representation in which syntactic information may be encoded and retrieved independently of semantic…

  18. Test-retest assessment of cortical activation induced by repetitive transcranial magnetic stimulation with brain atlas-guided optical topography

    NASA Astrophysics Data System (ADS)

    Tian, Fenghua; Kozel, F. Andrew; Yennu, Amarnath; Croarkin, Paul E.; McClintock, Shawn M.; Mapes, Kimberly S.; Husain, Mustafa M.; Liu, Hanli

    2012-11-01

    Repetitive transcranial magnetic stimulation (rTMS) is a technology that stimulates neurons with rapidly changing magnetic pulses with demonstrated therapeutic applications for various neuropsychiatric disorders. Functional near-infrared spectroscopy (fNIRS) is a suitable tool to assess rTMS-evoked brain responses without interference from the magnetic or electric fields generated by the TMS coil. We have previously reported a channel-wise study of combined rTMS/fNIRS on the motor and prefrontal cortices, showing a robust decrease of oxygenated hemoglobin concentration (Δ[HbO2]) at the sites of 1-Hz rTMS and the contralateral brain regions. However, the reliability of this putative clinical tool is unknown. In this study, we develop a rapid optical topography approach to spatially characterize the rTMS-evoked hemodynamic responses on a standard brain atlas. A hemispherical approximation of the brain is employed to convert the three-dimensional topography on the complex brain surface to a two-dimensional topography in the spherical coordinate system. The test-retest reliability of the combined rTMS/fNIRS is assessed using repeated measurements performed two to three days apart. The results demonstrate that the Δ[HbO2] amplitudes have moderate-to-high reliability at the group level; and the spatial patterns of the topographic images have high reproducibility in size and a moderate degree of overlap at the individual level.

  19. Technical and Organizational Considerations for the Long-Term Maintenance and Development of Digital Brain Atlases and Web-Based Databases

    PubMed Central

    Ito, Kei

    2010-01-01

    Digital brain atlas is a kind of image database that specifically provide information about neurons and glial cells in the brain. It has various advantages that are unmatched by conventional paper-based atlases. Such advantages, however, may become disadvantages if appropriate cares are not taken. Because digital atlases can provide unlimited amount of data, they should be designed to minimize redundancy and keep consistency of the records that may be added incrementally by different staffs. The fact that digital atlases can easily be revised necessitates a system to assure that users can access previous versions that might have been cited in papers at a particular period. To inherit our knowledge to our descendants, such databases should be maintained for a very long period, well over 100 years, like printed books and papers. Technical and organizational measures to enable long-term archive should be considered seriously. Compared to the initial development of the database, subsequent efforts to increase the quality and quantity of its contents are not regarded highly, because such tasks do not materialize in the form of publications. This fact strongly discourages continuous expansion of, and external contributions to, the digital atlases after its initial launch. To solve these problems, the role of the biocurators is vital. Appreciation of the scientific achievements of the people who do not write papers, and establishment of the secure academic career path for them, are indispensable for recruiting talents for this very important job. PMID:20661458

  20. Technical and organizational considerations for the long-term maintenance and development of digital brain atlases and web-based databases.

    PubMed

    Ito, Kei

    2010-01-01

    Digital brain atlas is a kind of image database that specifically provide information about neurons and glial cells in the brain. It has various advantages that are unmatched by conventional paper-based atlases. Such advantages, however, may become disadvantages if appropriate cares are not taken. Because digital atlases can provide unlimited amount of data, they should be designed to minimize redundancy and keep consistency of the records that may be added incrementally by different staffs. The fact that digital atlases can easily be revised necessitates a system to assure that users can access previous versions that might have been cited in papers at a particular period. To inherit our knowledge to our descendants, such databases should be maintained for a very long period, well over 100 years, like printed books and papers. Technical and organizational measures to enable long-term archive should be considered seriously. Compared to the initial development of the database, subsequent efforts to increase the quality and quantity of its contents are not regarded highly, because such tasks do not materialize in the form of publications. This fact strongly discourages continuous expansion of, and external contributions to, the digital atlases after its initial launch. To solve these problems, the role of the biocurators is vital. Appreciation of the scientific achievements of the people who do not write papers, and establishment of the secure academic career path for them, are indispensable for recruiting talents for this very important job.

  1. 3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas.

    PubMed

    Schubert, Nicole; Axer, Markus; Schober, Martin; Huynh, Anh-Minh; Huysegoms, Marcel; Palomero-Gallagher, Nicola; Bjaalie, Jan G; Leergaard, Trygve B; Kirlangic, Mehmet E; Amunts, Katrin; Zilles, Karl

    2016-01-01

    High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains. This paper provides a newly developed pipeline combining imaging and reconstruction steps with a novel registration strategy to integrate new neuroimaging modalities into the Waxholm Space atlas. As a proof of principle, we incorporated large scale high-resolution cyto-, muscarinic M2 receptor, and fiber architectonic images of rat brains into the 3D digital MRI based atlas of the Sprague Dawley rat in Waxholm Space. We describe the whole workflow, from image acquisition to reconstruction and registration of these three modalities into the Waxholm Space rat atlas. The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations. The validity of the procedure is qualitatively demonstrated by visual inspection, and a quantitative evaluation is performed by measurement of the concordance between representative atlas-delineated regions and the same regions based on receptor or fiber architectonic data. This novel approach enables for the first time the generation of 3D reconstructed volumes of nerve fibers and fiber tracts, or of muscarinic M2 receptor density distributions, in an entire rat brain. Additionally, our pipeline facilitates the inclusion of further neuroimaging datasets, e.g., 3D reconstructed volumes of histochemical stainings or of the regional distributions of multiple other receptor types, into the Waxholm Space

  2. 3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas

    PubMed Central

    Schubert, Nicole; Axer, Markus; Schober, Martin; Huynh, Anh-Minh; Huysegoms, Marcel; Palomero-Gallagher, Nicola; Bjaalie, Jan G.; Leergaard, Trygve B.; Kirlangic, Mehmet E.; Amunts, Katrin; Zilles, Karl

    2016-01-01

    High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains. This paper provides a newly developed pipeline combining imaging and reconstruction steps with a novel registration strategy to integrate new neuroimaging modalities into the Waxholm Space atlas. As a proof of principle, we incorporated large scale high-resolution cyto-, muscarinic M2 receptor, and fiber architectonic images of rat brains into the 3D digital MRI based atlas of the Sprague Dawley rat in Waxholm Space. We describe the whole workflow, from image acquisition to reconstruction and registration of these three modalities into the Waxholm Space rat atlas. The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations. The validity of the procedure is qualitatively demonstrated by visual inspection, and a quantitative evaluation is performed by measurement of the concordance between representative atlas-delineated regions and the same regions based on receptor or fiber architectonic data. This novel approach enables for the first time the generation of 3D reconstructed volumes of nerve fibers and fiber tracts, or of muscarinic M2 receptor density distributions, in an entire rat brain. Additionally, our pipeline facilitates the inclusion of further neuroimaging datasets, e.g., 3D reconstructed volumes of histochemical stainings or of the regional distributions of multiple other receptor types, into the Waxholm Space

  3. Phosphine Catalysis of Allenes with Electrophiles

    PubMed Central

    Wang, Zhiming; Xu, Xingzhu; Kwon, Ohyun

    2014-01-01

    Nucleophilic phosphine catalysis of allenes with electrophiles is one of the most powerful and straightforward synthetic strategies for the generation of highly functionalized carbocycle or heterocycle structural motifs, which are present in a wide range of bioactive natural products and medicinally important substances. The reaction topologies can be controlled through judicious choice of the phosphine catalyst and the structural variations of starting materials. This Tutorial Review presents selected examples of nucleophilic phosphine catalysis using allenes and electrophiles. PMID:24663290

  4. Van Allen Discovery Most Important

    NASA Technical Reports Server (NTRS)

    Jastrow, R.

    1959-01-01

    The first step toward the exploration of space occurred approximately 22 months ago as a part of the International Geophysical Year. In the short interval since October, 1957, the new tools of research, the satellite and the space rocket, have produced two unexpected results of fundamental scientific importance. First, instruments placed in the Explorer satellites by James A. Van Allen have revealed the existence of layers of energetic particles in the outer atmosphere. This discovery constitutes the most significant research achievement of the IGY satellite program. The layers may provide the explanation for the aurora and other geophysical phenomena, and they will also influence the design of vehicles for manned space flight, whose occupants must be shielded against their harmful biological effects. Second, the shape of the earth has been determined very accurately with the aid of data from the first Vanguard. As a result of this investigation, we have found that our planet tends toward the shape of a pear, with its stem at the North Pole. This discovery may produce major changes in our ideas on the interior structure of the earth.

  5. Unbiased group-wise image registration: applications in brain fiber tract atlas construction and functional connectivity analysis.

    PubMed

    Geng, Xiujuan; Gu, Hong; Shin, Wanyong; Ross, Thomas J; Yang, Yihong

    2011-10-01

    We propose an unbiased implicit-reference group-wise (IRG) image registration method and demonstrate its applications in the construction of a brain white matter fiber tract atlas and the analysis of resting-state functional MRI (fMRI) connectivity. Most image registration techniques pair-wise align images to a selected reference image and group analyses are performed in the reference space, which may produce bias. The proposed method jointly estimates transformations, with an elastic deformation model, registering all images to an implicit reference corresponding to the group average. The unbiased registration is applied to build a fiber tract atlas by registering a group of diffusion tensor images. Compared to reference-based registration, the IRG registration improves the fiber track overlap within the group. After applying the method in the fMRI connectivity analysis, results suggest a general improvement in functional connectivity maps at a group level in terms of larger cluster size and higher average t-scores.

  6. A whole-brain atlas of inputs to serotonergic neurons of the dorsal and median raphe nuclei.

    PubMed

    Pollak Dorocic, Iskra; Fürth, Daniel; Xuan, Yang; Johansson, Yvonne; Pozzi, Laura; Silberberg, Gilad; Carlén, Marie; Meletis, Konstantinos

    2014-08-01

    The serotonin system is proposed to regulate physiology and behavior and to underlie mood disorders; nevertheless, the circuitry controlling serotonergic neurons remains uncharacterized. We therefore generated a comprehensive whole-brain atlas defining the monosynaptic inputs onto forebrain-projecting serotonergic neurons of dorsal versus median raphe based on a genetically restricted transsynaptic retrograde tracing strategy. We identified discrete inputs onto serotonergic neurons from forebrain and brainstem neurons, with specific inputs from hypothalamus, cortex, basal ganglia, and midbrain, displaying a greater than anticipated complexity and diversity in cell-type-specific connectivity. We identified and functionally confirmed monosynaptic glutamatergic inputs from prefrontal cortex and lateral habenula onto serotonergic neurons as well as a direct GABAergic input from striatal projection neurons. In summary, our findings emphasize the role of hyperdirect inputs to serotonergic neurons. Cell-type-specific classification of connectivity patterns will allow for further functional analysis of the diverse but specific inputs that control serotonergic neurons during behavior.

  7. ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain

    PubMed Central

    Prüfer, Kay; Kelso, Janet; Dannemann, Michael

    2016-01-01

    Summary: We present ABAEnrichment, an R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas. We validate ABAEnrichment by successfully recovering the origin of gene sets identified in specific brain cell-types and developmental stages. Availability and Implementation: ABAEnrichment was implemented as an R package and is available under GPL (≥ 2) from the Bioconductor website (http://bioconductor.org/packages/3.3/bioc/html/ABAEnrichment.html). Contacts: steffi_grote@eva.mpg.de, kelso@eva.mpg.de or michael_dannemann@eva.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354695

  8. kNN-based multi-spectral MRI brain tissue classification: manual training versus automated atlas-based training

    NASA Astrophysics Data System (ADS)

    Vrooman, Henri A.; Cocosco, Chris A.; Stokking, Rik; Ikram, M. Arfan; Vernooij, Meike W.; Breteler, Monique M.; Niessen, Wiro J.

    2006-03-01

    Conventional k-Nearest-Neighbor (kNN) classification, which has been successfully applied to classify brain tissue, requires laborious training on manually labeled subjects. In this work, the performance of kNN-based segmentation of gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF) using manual training is compared with a new method, in which training is automated using an atlas. From 12 subjects, standard T2 and PD scans and a high-resolution, high-contrast scan (Siemens T1-weighted HASTE sequence with reverse contrast) were used as feature sets. For the conventional kNN method, manual segmentations were used for training, and classifications were evaluated in a leave-one-out study. The performance as a function of the number of samples per tissue, and k was studied. For fully automated training, scans were registered to a probabilistic brain atlas. Initial training samples were randomly selected per tissue based on a threshold on the tissue probability. These initials were processed to keep the most reliable samples. Performance of the method for varying the threshold on the tissue probability method was studied. By measuring the percentage overlap (SI), classification results of both methods were validated. For conventional kNN classification, varying the number of training samples did not result in significant differences, while increasing k gave significantly better results. In the method using automated training, there is an overestimation of GM at the expense of CSF at higher thresholds on the tissue probability maps. The difference between the conventional method (k=45) and the observers was not significantly larger than inter-observer variability for all tissue types. The automated method performed slightly worse and performed equal to the observers for WM, and less for CSF and GM. From these results it can be concluded that conventional kNN classification may replace manual segmentation, and that atlas-based kNN segmentation has strong

  9. Electrophilic addition and cyclization reactions of allenes.

    PubMed

    Ma, Shengming

    2009-10-20

    Modern organic synthesis depends on the development of highly selective methods for the efficient construction of potentially useful target molecules. A primary goal in our laboratory is the discovery of new reactions that convert readily available starting materials to complex products with complete control of regio- and stereoselectivity. Allenes are one underused moiety in organic synthesis, because these groups are often thought to be highly reactive. However, many compounds containing the allene group, including natural products and pharmaceuticals, are fairly stable. The chemistry of allenes has been shown to have significant potential in organic synthesis. Electrophilic additions to allenes have often been considered to be synthetically less attractive due to the lack of efficient control of the regio- and stereoselectivity. However, this Account describes electrophilic reactions of allenes with defined regio- and stereoselectivity developed in our laboratory. Many substituted allenes are readily available from propargylic alcohols. Our work has involved an exploration of the reactions of these allenes with many different electrophiles: the E- or Z-halo- or seleno-hydroxylations of allenyl sulfoxides, sulfones, phosphine oxides, carboxylates, sulfides or selenides, butenolides, and arenes, and the halo- or selenolactonization reactions of allenoic acids and allenoates. These reactions have produced a host of new compounds such as stereodefined allylic alcohols, ethers, amides, thiiranes, and lactones. In all these reactions, water acts as a reactant and plays an important role in determining the reaction pathway and the stereoselectivity. The differing electronic properties of the two C=C bonds in these allenes determine the regioselectivity of these reactions. Through mechanistic studies of chirality transfer, isolation and reactivity of cyclic intermediates, (18)O-labeling, and substituent effects, we discovered that the E-stereoselectivity of some

  10. Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain

    PubMed Central

    French, Leon; Pavlidis, Paul

    2011-01-01

    We studied the global relationship between gene expression and neuroanatomical connectivity in the adult rodent brain. We utilized a large data set of the rat brain “connectome” from the Brain Architecture Management System (942 brain regions and over 5000 connections) and used statistical approaches to relate the data to the gene expression signatures of 17,530 genes in 142 anatomical regions from the Allen Brain Atlas. Our analysis shows that adult gene expression signatures have a statistically significant relationship to connectivity. In particular, brain regions that have similar expression profiles tend to have similar connectivity profiles, and this effect is not entirely attributable to spatial correlations. In addition, brain regions which are connected have more similar expression patterns. Using a simple optimization approach, we identified a set of genes most correlated with neuroanatomical connectivity, and find that this set is enriched for genes involved in neuronal development and axon guidance. A number of the genes have been implicated in neurodevelopmental disorders such as autistic spectrum disorder. Our results have the potential to shed light on the role of gene expression patterns in influencing neuronal activity and connectivity, with potential applications to our understanding of brain disorders. Supplementary data are available at http://www.chibi.ubc.ca/ABAMS. PMID:21253556

  11. Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas1,2,3

    PubMed Central

    Borg, Jana Schaich; Vu, Mai-Anh; Badea, Cristian; Badea, Alexandra; Johnson, G. Allan

    2015-01-01

    Abstract Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest because of the insight they can provide about spatially distributed neural circuitry. The promise of such recordings has inspired great progress in methods for surgically implanting large numbers of metal electrodes into intact rodent brains. However, methods for localizing the precise location of these electrodes have remained severely lacking. Traditional histological techniques that require slicing and staining of physical brain tissue are cumbersome and become increasingly impractical as the number of implanted electrodes increases. Here we solve these problems by describing a method that registers 3D computed tomography (CT) images of intact rat brains implanted with metal electrode bundles to a magnetic resonance imaging histology (MRH) atlas. Our method allows accurate visualization of each electrode bundle’s trajectory and location without removing the electrodes from the brain or surgically implanting external markers. In addition, unlike physical brain slices, once the 3D images of the electrode bundles and the MRH atlas are registered, it is possible to verify electrode placements from many angles by “reslicing” the images along different planes of view. Furthermore, our method can be fully automated and easily scaled to applications with large numbers of specimens. Our digital imaging approach to efficiently localizing metal electrodes offers a substantial addition to currently available methods, which, in turn, may help accelerate the rate at which insights are gleaned from rodent network neuroscience. PMID:26322331

  12. Preparation of allenic sulfones and allenes from the selenosulfonation of acetylenes

    SciTech Connect

    Back, T.G.; Krishna, M.V.; Muralidharan, K.R. )

    1989-08-18

    {beta}-(phenylseleno)vinyl sulfones 2 are readily obtained from the free-radical selenosulfonation of acetylenes. Compounds 2 isomerize to allyl sulfones 4 under base-catalyzed conditions in nearly quantitative yield, with high stereoselectivity favoring the Z configuration. Allyl sulfones 4 afford generally high yields of allenic sulfones 1 when subjected to oxidation with m-chloroperbenzoic acid or tert-butyl hydroperoxide, followed by selenoxide syn-elimination. The sulfone-stabilized anion intermediates in the isomerizations of 2 to 4 can be alkylated, deuterated, or silylated in the {alpha}-position prior to oxidation, providing allenic sulfones with an additional {alpha}-substituent. In some cases, spontaneous elimination of the phenylseleno group occurred, producing the allenic sulfone without the need for an oxidation step. Desulfonylation of allyl sulfones 4f, 4c, and 25 with sodium amalgam afforded vinyl selenides that were converted to allenes in moderate to good yields by oxidation-elimination. The copper-catalyzed coupling of allyl sulfones 4 with Grignard reagents comprises an alternative route to vinyl selenide precursors of allenes. These procedures permit the synthesis of various {alpha}- and {gamma}-substituted allenic sulfones and allenes from acetylenes.

  13. Mechanisms of allene stereoinversion by imidozirconium complexes.

    PubMed

    Michael, Forrest E; Duncan, Andrew P; Sweeney, Zachary K; Bergman, Robert G

    2003-06-18

    The zirconium-mediated stereoinversion of allenes has been investigated by studying the stereochemical behavior of metallacycles derived from [2 + 2] cycloaddition of enantioenriched allenes with chiral and achiral imidozirconocene complexes. Relative rates of metallacycle racemization were measured by circular dichroism, and intermediates in the selective stereoinversion of diphenylallene with a chiral imidozirconium complex were observed by NMR spectroscopy. Metallacycles derived from dialkylallenes are proposed to racemize via reversible beta-hydride elimination. Stereoinversion of diarylallene-derived metallacycles proceeds much more slowly and is thought to proceed through an eta4-azatrimethylenemethane transition state.

  14. Brain in situ hybridization maps as a source for reverse-engineering transcriptional regulatory networks: Alzheimer's disease insights.

    PubMed

    Acquaah-Mensah, George K; Taylor, Ronald C

    2016-07-15

    Microarray data have been a valuable resource for identifying transcriptional regulatory relationships among genes. As an example, brain region-specific transcriptional regulatory events have the potential of providing etiological insights into Alzheimer Disease (AD). However, there is often a paucity of suitable brain-region specific expression data obtained via microarrays or other high throughput means. The Allen Brain Atlas in situ hybridization (ISH) data sets (Jones et al., 2009) represent a potentially valuable alternative source of high-throughput brain region-specific gene expression data for such purposes. In this study, Allen Brain Atlas mouse ISH data in the hippocampal fields were extracted, focusing on 508 genes relevant to neurodegeneration. Transcriptional regulatory networks were learned using three high-performing network inference algorithms. Only 17% of regulatory edges from a network reverse-engineered based on brain region-specific ISH data were also found in a network constructed upon gene expression correlations in mouse whole brain microarrays, thus showing the specificity of gene expression within brain sub-regions. Furthermore, the ISH data-based networks were used to identify instructive transcriptional regulatory relationships. Ncor2, Sp3 and Usf2 form a unique three-party regulatory motif, potentially affecting memory formation pathways. Nfe2l1, Egr1 and Usf2 emerge among regulators of genes involved in AD (e.g. Dhcr24, Aplp2, Tia1, Pdrx1, Vdac1, and Syn2). Further, Nfe2l1, Egr1 and Usf2 are sensitive to dietary factors and could be among links between dietary influences and genes in the AD etiology. Thus, this approach of harnessing brain region-specific ISH data represents a rare opportunity for gleaning unique etiological insights for diseases such as AD.

  15. Recent developments in allene-based synthetic methods.

    PubMed

    Kim, Hiyun; Williams, Lawrence J

    2008-11-01

    Presented is a review of the advances in synthetic methodology that make use of the allene functional group, with emphasis on catalytic asymmetric transformations and new mechanistic insights. The review covers the period from January 2007 to May 2008 and focuses on intra- and intermolecular cycloaddition, carbocycle cycloisomerization, heterocycle synthesis, epoxidation, addition and miscellaneous transformations. A brief discussion of allenes as transition metal ligands, the use of allenes in total synthesis and potential medicinal agents that contain the allene functionality is also presented.

  16. Atlas based brain volumetry: How to distinguish regional volume changes due to biological or physiological effects from inherent noise of the methodology.

    PubMed

    Opfer, Roland; Suppa, Per; Kepp, Timo; Spies, Lothar; Schippling, Sven; Huppertz, Hans-Jürgen

    2016-05-01

    Fully-automated regional brain volumetry based on structural magnetic resonance imaging (MRI) plays an important role in quantitative neuroimaging. In clinical trials as well as in clinical routine multiple MRIs of individual patients at different time points need to be assessed longitudinally. Measures of inter- and intrascanner variability are crucial to understand the intrinsic variability of the method and to distinguish volume changes due to biological or physiological effects from inherent noise of the methodology. To measure regional brain volumes an atlas based volumetry (ABV) approach was deployed using a highly elastic registration framework and an anatomical atlas in a well-defined template space. We assessed inter- and intrascanner variability of the method in 51 cognitively normal subjects and 27 Alzheimer dementia (AD) patients from the Alzheimer's Disease Neuroimaging Initiative by studying volumetric results of repeated scans for 17 compartments and brain regions. Median percentage volume differences of scan-rescans from the same scanner ranged from 0.24% (whole brain parenchyma in healthy subjects) to 1.73% (occipital lobe white matter in AD), with generally higher differences in AD patients as compared to normal subjects (e.g., 1.01% vs. 0.78% for the hippocampus). Minimum percentage volume differences detectable with an error probability of 5% were in the one-digit percentage range for almost all structures investigated, with most of them being below 5%. Intrascanner variability was independent of magnetic field strength. The median interscanner variability was up to ten times higher than the intrascanner variability.

  17. Atlas of transgenic Tet-Off Ca2+/calmodulin-dependent protein kinase II and prion protein promoter activity in the mouse brain.

    PubMed

    Odeh, Francis; Leergaard, Trygve B; Boy, Jana; Schmidt, Thorsten; Riess, Olaf; Bjaalie, Jan G

    2011-02-14

    Conditional transgenic mouse models are important tools for investigations of neurodegenerative diseases and evaluation of potential therapeutic interventions. A popular conditional transgenic system is the binary tetracycline-responsive gene (Tet-Off) system, in which the expression of the gene of interest depends on a tetracycline-regulatable transactivator (tTA) under the control of a specific promoter construct. The most frequently used Tet-Off promoter mouse lines are the Ca(2+)/calmodulin-dependent protein kinase II (CamKII) and prion protein (PrP) promoter lines, respectively. To target the regulated gene of interest to relevant brain regions, a priori knowledge about the spatial distribution of the regulated gene expression in the brain is important. Such distribution patterns can be investigated using double transgenic mice in which the promoter construct regulates a LacZ reporter gene encoding the marker β-galactosidase which can be histologically detected using its substrate X-gal. We have previously published an atlas showing the brain-wide expression mediated by the Tet-Off PrP promoter mouse line, but the distribution of activity in the Tet-Off CamKII promoter mouse line is less well known. To compare promoter activity distributions in these two Tet-Off mouse lines, we have developed an online digital atlas tailored for side-by-side comparison of histological section images. The atlas provides a comprehensive list of brain regions containing X-gal labeling and an interactive dual image viewer tool for panning and zooming of corresponding section images. Comparison of spatial expression patterns between the two lines show considerable regional and cellular differences, relevant in context of generation and analysis of inducible models based on these two tetracycline responsive promoter mouse lines.

  18. NeuroVault.org: A repository for sharing unthresholded statistical maps, parcellations, and atlases of the human brain.

    PubMed

    Gorgolewski, Krzysztof J; Varoquaux, Gael; Rivera, Gabriel; Schwartz, Yannick; Sochat, Vanessa V; Ghosh, Satrajit S; Maumet, Camille; Nichols, Thomas E; Poline, Jean-Baptiste; Yarkoni, Tal; Margulies, Daniel S; Poldrack, Russell A

    2016-01-01

    NeuroVault.org is dedicated to storing outputs of analyses in the form of statistical maps, parcellations and atlases, a unique strategy that contrasts with most neuroimaging repositories that store raw acquisition data or stereotaxic coordinates. Such maps are indispensable for performing meta-analyses, validating novel methodology, and deciding on precise outlines for regions of interest (ROIs). NeuroVault is open to maps derived from both healthy and clinical populations, as well as from various imaging modalities (sMRI, fMRI, EEG, MEG, PET, etc.). The repository uses modern web technologies such as interactive web-based visualization, cognitive decoding, and comparison with other maps to provide researchers with efficient, intuitive tools to improve the understanding of their results. Each dataset and map is assigned a permanent Universal Resource Locator (URL), and all of the data is accessible through a REST Application Programming Interface (API). Additionally, the repository supports the NIDM-Results standard and has the ability to parse outputs from popular FSL and SPM software packages to automatically extract relevant metadata. This ease of use, modern web-integration, and pioneering functionality holds promise to improve the workflow for making inferences about and sharing whole-brain statistical maps.

  19. NeuroVault.org: A repository for sharing unthresholded statistical maps, parcellations, and atlases of the human brain.

    PubMed

    Gorgolewski, Krzysztof J; Varoquaux, Gael; Rivera, Gabriel; Schwartz, Yannick; Sochat, Vanessa V; Ghosh, Satrajit S; Maumet, Camille; Nichols, Thomas E; Poline, Jean-Baptiste; Yarkoni, Tal; Margulies, Daniel S; Poldrack, Russell A

    2016-01-01

    NeuroVault.org is dedicated to storing outputs of analyses in the form of statistical maps, parcellations and atlases, a unique strategy that contrasts with most neuroimaging repositories that store raw acquisition data or stereotaxic coordinates. Such maps are indispensable for performing meta-analyses, validating novel methodology, and deciding on precise outlines for regions of interest (ROIs). NeuroVault is open to maps derived from both healthy and clinical populations, as well as from various imaging modalities (sMRI, fMRI, EEG, MEG, PET, etc.). The repository uses modern web technologies such as interactive web-based visualization, cognitive decoding, and comparison with other maps to provide researchers with efficient, intuitive tools to improve the understanding of their results. Each dataset and map is assigned a permanent Universal Resource Locator (URL), and all of the data is accessible through a REST Application Programming Interface (API). Additionally, the repository supports the NIDM-Results standard and has the ability to parse outputs from popular FSL and SPM software packages to automatically extract relevant metadata. This ease of use, modern web-integration, and pioneering functionality holds promise to improve the workflow for making inferences about and sharing whole-brain statistical maps. PMID:25869863

  20. Bayesian longitudinal segmentation of hippocampal substructures in brain MRI using subject-specific atlases.

    PubMed

    Iglesias, Juan Eugenio; Van Leemput, Koen; Augustinack, Jean; Insausti, Ricardo; Fischl, Bruce; Reuter, Martin

    2016-11-01

    The hippocampal formation is a complex, heterogeneous structure that consists of a number of distinct, interacting subregions. Atrophy of these subregions is implied in a variety of neurodegenerative diseases, most prominently in Alzheimer's disease (AD). Thanks to the increasing resolution of MR images and computational atlases, automatic segmentation of hippocampal subregions is becoming feasible in MRI scans. Here we introduce a generative model for dedicated longitudinal segmentation that relies on subject-specific atlases. The segmentations of the scans at the different time points are jointly computed using Bayesian inference. All time points are treated the same to avoid processing bias. We evaluate this approach using over 4700 scans from two publicly available datasets (ADNI and MIRIAD). In test-retest reliability experiments, the proposed method yielded significantly lower volume differences and significantly higher Dice overlaps than the cross-sectional approach for nearly every subregion (average across subregions: 4.5% vs. 6.5%, Dice overlap: 81.8% vs. 75.4%). The longitudinal algorithm also demonstrated increased sensitivity to group differences: in MIRIAD (69 subjects: 46 with AD and 23 controls), it found differences in atrophy rates between AD and controls that the cross sectional method could not detect in a number of subregions: right parasubiculum, left and right presubiculum, right subiculum, left dentate gyrus, left CA4, left HATA and right tail. In ADNI (836 subjects: 369 with AD, 215 with early cognitive impairment - eMCI - and 252 controls), all methods found significant differences between AD and controls, but the proposed longitudinal algorithm detected differences between controls and eMCI and differences between eMCI and AD that the cross sectional method could not find: left presubiculum, right subiculum, left and right parasubiculum, left and right HATA. Moreover, many of the differences that the cross-sectional method already found

  1. Bayesian longitudinal segmentation of hippocampal substructures in brain MRI using subject-specific atlases.

    PubMed

    Iglesias, Juan Eugenio; Van Leemput, Koen; Augustinack, Jean; Insausti, Ricardo; Fischl, Bruce; Reuter, Martin

    2016-11-01

    The hippocampal formation is a complex, heterogeneous structure that consists of a number of distinct, interacting subregions. Atrophy of these subregions is implied in a variety of neurodegenerative diseases, most prominently in Alzheimer's disease (AD). Thanks to the increasing resolution of MR images and computational atlases, automatic segmentation of hippocampal subregions is becoming feasible in MRI scans. Here we introduce a generative model for dedicated longitudinal segmentation that relies on subject-specific atlases. The segmentations of the scans at the different time points are jointly computed using Bayesian inference. All time points are treated the same to avoid processing bias. We evaluate this approach using over 4700 scans from two publicly available datasets (ADNI and MIRIAD). In test-retest reliability experiments, the proposed method yielded significantly lower volume differences and significantly higher Dice overlaps than the cross-sectional approach for nearly every subregion (average across subregions: 4.5% vs. 6.5%, Dice overlap: 81.8% vs. 75.4%). The longitudinal algorithm also demonstrated increased sensitivity to group differences: in MIRIAD (69 subjects: 46 with AD and 23 controls), it found differences in atrophy rates between AD and controls that the cross sectional method could not detect in a number of subregions: right parasubiculum, left and right presubiculum, right subiculum, left dentate gyrus, left CA4, left HATA and right tail. In ADNI (836 subjects: 369 with AD, 215 with early cognitive impairment - eMCI - and 252 controls), all methods found significant differences between AD and controls, but the proposed longitudinal algorithm detected differences between controls and eMCI and differences between eMCI and AD that the cross sectional method could not find: left presubiculum, right subiculum, left and right parasubiculum, left and right HATA. Moreover, many of the differences that the cross-sectional method already found

  2. An integrative analysis of regional gene expression profiles in the human brain.

    PubMed

    Myers, Emma M; Bartlett, Christopher W; Machiraju, Raghu; Bohland, Jason W

    2015-02-01

    Studies of the brain's transcriptome have become prominent in recent years, resulting in an accumulation of datasets with somewhat distinct attributes. These datasets, which are often analyzed only in isolation, also are often collected with divergent goals, which are reflected in their sampling properties. While many researchers have been interested in sampling gene expression in one or a few brain areas in a large number of subjects, recent efforts from the Allen Institute for Brain Sciences and others have focused instead on dense neuroanatomical sampling, necessarily limiting the number of individual donor brains studied. The purpose of the present work is to develop methods that draw on the complementary strengths of these two types of datasets for study of the human brain, and to characterize the anatomical specificity of gene expression profiles and gene co-expression networks derived from human brains using different specific technologies. The approach is applied using two publicly accessible datasets: (1) the high anatomical resolution Allen Human Brain Atlas (AHBA, Hawrylycz et al., 2012) and (2) a relatively large sample size, but comparatively coarse neuroanatomical dataset described previously by Gibbs et al. (2010). We found a relatively high degree of correspondence in differentially expressed genes and regional gene expression profiles across the two datasets. Gene co-expression networks defined in individual brain regions were less congruent, but also showed modest anatomical specificity. Using gene modules derived from the Gibbs dataset and from curated gene lists, we demonstrated varying degrees of anatomical specificity based on two classes of methods, one focused on network modularity and the other focused on enrichment of expression levels. Two approaches to assessing the statistical significance of a gene set's modularity in a given brain region were studied, which provide complementary information about the anatomical specificity of a gene

  3. H. Julian Allen with Blunt Body Theory

    NASA Technical Reports Server (NTRS)

    1957-01-01

    H. Julian Allen is best known for his 'Blunt Body Theory' of aerodynamics, a design technique for alleviating the severe re-entry heating problem which was then delaying the development of ballistic missiles. His findings revolutionized the fundamental design of ballistic missle re-entry shapes. Subsequently, applied research led to applications of the 'blunt' shape to ballistic missles and spacecraft which were intended to re-enter the Earth's atmosphere. This application led to the design of ablative heat shields that protected the Mercury, Gemini and Apollo astronauts as their space capsules re- entered the Earth's atmosphere. 'Harvey' Allen as he was called by most, was not only a brilliant scientist and aeronautical engineer but was also admired for his kindness, thoughtfulness and sense of humor. Among his many other accomplishments, Harvey Allen served as Center Director of the NASA Ames Research Center from 1965 to 1969. He died of a heart attack on January 29, 1977 at the age of 66.

  4. High-resolution prediction of mouse brain connectivity using gene expression patterns.

    PubMed

    Fakhry, Ahmed; Ji, Shuiwang

    2015-02-01

    The brain is a multi-level system in which the high-level functions are generated by low-level genetic mechanisms. Thus, elucidating the relationship among multiple brain levels via correlative and predictive analytics is an important area in brain research. Currently, studies in multiple species have indicated that the spatiotemporal gene expression patterns are predictive of brain wiring. Specifically, results on the worm Caenorhabditis elegans have shown that the prediction of neuronal connectivity using gene expression signatures yielded statistically significant results. Recent studies on the mammalian brain produced similar results at the coarse regional level. In this study, we provide the first high-resolution, large-scale integrative analysis of the transcriptome and connectome in a single mammalian brain at a fine voxel level. By using the Allen Brain Atlas data, we predict voxel-level brain connectivity based on the gene expressions in the adult mouse brain. We employ regularized models to show that gene expression is predictive of connectivity at the voxel-level with an accuracy of 93%. We also identify a set of genes playing the most important role in connectivity prediction. We use only this small number of genes to predict the brain wiring with an accuracy over 80%. We discover that these important genes are enriched in neurons as compared to glia, and they perform connectivity-related functions. We perform several interesting correlative studies to further elucidate the transcriptome-connectome relationship.

  5. Global differential expression of genes located in the Down Syndrome Critical Region in normal human brain

    PubMed Central

    Montoya, Julio Cesar; Fajardo, Dianora; Peña, Angela; Sánchez, Adalberto; Domínguez, Martha C; Satizábal, José María

    2014-01-01

    Background: The information of gene expression obtained from databases, have made possible the extraction and analysis of data related with several molecular processes involving not only in brain homeostasis but its disruption in some neuropathologies; principally in Down syndrome and the Alzheimer disease. Objective: To correlate the levels of transcription of 19 genes located in the Down Syndrome Critical Region (DSCR) with their expression in several substructures of normal human brain. Methods: There were obtained expression profiles of 19 DSCR genes in 42 brain substructures, from gene expression values available at the database of the human brain of the Brain Atlas of the Allen Institute for Brain Sciences", (http://human.brain-map.org/). The co-expression patterns of DSCR genes in brain were calculated by using multivariate statistical methods. Results: Highest levels of gene expression were registered at caudate nucleus, nucleus accumbens and putamen among central areas of cerebral cortex. Increased expression levels of RCAN1 that encode by a protein involved in signal transduction process of the CNS were recorded for PCP4 that participates in the binding to calmodulin and TTC3; a protein that is associated with differentiation of neurons. That previously identified brain structures play a crucial role in the learning process, in different class of memory and in motor skills. Conclusion: The precise regulation of DSCR gene expression is crucial to maintain the brain homeostasis, especially in those areas with high levels of gene expression associated with a remarkable process of learning and cognition. PMID:25767303

  6. Maximal tractable subclasses of Allen`s interval algebra: Preliminary report

    SciTech Connect

    Drakengren, T.; Jonsson, P.

    1996-12-31

    This paper continues Nebel and Burckert`s investigation of Allen`s interval algebra by presenting nine more maximal tractable subclasses of the algebra (provided that P {ne} NP), in addition to their previously reported ORD-Horn subclass. Furthermore, twelve tractable subclasses are identified, whose maximality is riot decided. Four of these can express the notion of sequentiality between intervals, which is not possible in the ORD-Horn algebra. The satisfiability algorithm, which is common for all the algebras, is shown to be linear.

  7. Automated anatomical interpretation of ion distributions in tissue: linking imaging mass spectrometry to curated atlases.

    PubMed

    Verbeeck, Nico; Yang, Junhai; De Moor, Bart; Caprioli, Richard M; Waelkens, Etienne; Van de Plas, Raf

    2014-09-16

    Imaging mass spectrometry (IMS) has become a prime tool for studying the distribution of biomolecules in tissue. Although IMS data sets can become very large, computational methods have made it practically feasible to search these experiments for relevant findings. However, these methods lack access to an important source of information that many human interpretations rely upon: anatomical insight. In this work, we address this need by (1) integrating a curated anatomical data source with an empirically acquired IMS data source, establishing an algorithm-accessible link between them and (2) demonstrating the potential of such an IMS-anatomical atlas link by applying it toward automated anatomical interpretation of ion distributions in tissue. The concept is demonstrated in mouse brain tissue, using the Allen Mouse Brain Atlas as the curated anatomical data source that is linked to MALDI-based IMS experiments. We first develop a method to spatially map the anatomical atlas to the IMS data sets using nonrigid registration techniques. Once a mapping is established, a second computational method, called correlation-based querying, gives an elementary demonstration of the link by delivering basic insight into relationships between ion images and anatomical structures. Finally, a third algorithm moves further beyond both registration and correlation by providing automated anatomical interpretation of ion images. This task is approached as an optimization problem that deconstructs ion distributions as combinations of known anatomical structures. We demonstrate that establishing a link between an IMS experiment and an anatomical atlas enables automated anatomical annotation, which can serve as an important accelerator both for human and machine-guided exploration of IMS experiments.

  8. Cross-coupling/cyclization reactions of two different allenic moieties.

    PubMed

    Alcaide, Benito; Almendros, Pedro; Martínez del Campo, Teresa

    2010-05-25

    The allene moiety represents an excellent building block for allene cross-coupling cyclization reactions, affording heterocyclic skeletons in a single step. This strategy is of particular interest when two different allene derivatives are involved in a series of metal-catalyzed cross-coupling heterocyclization processes. This Concept article is focused on the Pd-catalyzed union of two different allenic moieties, with cyclization of at least one of them by intramolecular cyclometalation. These new, versatile, and highly effective transformations are complex multistep processes leading to potential privileged structures that could find wide applications in related medicinal chemistry.

  9. 5. Historic American Buildings Survey Harold Allen, Photographer 19 June ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Historic American Buildings Survey Harold Allen, Photographer 19 June 1965 ICONOSTASIS AND CHANDELIER - Holy Trinity Russian & Greek Orthodox Church, 1121 North Leavitt Street, Chicago, Cook County, IL

  10. 4. Historic American Buildings Survey Harold Allen, Photographer 19 June ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. Historic American Buildings Survey Harold Allen, Photographer 19 June 1965 SANCTUARY FROM ENTRANCE - Holy Trinity Russian & Greek Orthodox Church, 1121 North Leavitt Street, Chicago, Cook County, IL

  11. A chemical proteomic atlas of brain serine hydrolases identifies cell type-specific pathways regulating neuroinflammation

    PubMed Central

    Viader, Andreu; Ogasawara, Daisuke; Joslyn, Christopher M; Sanchez-Alavez, Manuel; Mori, Simone; Nguyen, William; Conti, Bruno; Cravatt, Benjamin F

    2016-01-01

    Metabolic specialization among major brain cell types is central to nervous system function and determined in large part by the cellular distribution of enzymes. Serine hydrolases are a diverse enzyme class that plays fundamental roles in CNS metabolism and signaling. Here, we perform an activity-based proteomic analysis of primary mouse neurons, astrocytes, and microglia to furnish a global portrait of the cellular anatomy of serine hydrolases in the brain. We uncover compelling evidence for the cellular compartmentalization of key chemical transmission pathways, including the functional segregation of endocannabinoid (eCB) biosynthetic enzymes diacylglycerol lipase-alpha (DAGLα) and –beta (DAGLβ) to neurons and microglia, respectively. Disruption of DAGLβ perturbed eCB-eicosanoid crosstalk specifically in microglia and suppressed neuroinflammatory events in vivo independently of broader effects on eCB content. Mapping the cellular distribution of metabolic enzymes thus identifies pathways for regulating specialized inflammatory responses in the brain while avoiding global alterations in CNS function. DOI: http://dx.doi.org/10.7554/eLife.12345.001 PMID:26779719

  12. Computer tomographic imaging and anatomic correlation of the human brain: A comparative atlas of thin CT-scan sections and correlated neuro-anatomic preparations

    SciTech Connect

    Plets, C.; Baert, A.L.; Nijs, G.L.; Wilms, G.

    1986-01-01

    It is of the greatest importance to the radiologist, the neurologist and the neurosurgeon to be able to localize topographically a pathological brain process on the CT scan as precisely as possible. For that purpose, the identification of as many anatomical structures as possible on the CT scan image are necessary and indispensable. In this atlas a great number of detailed anatomical data on frontal horizontal CT scan sections, each being only 2 mm thick, are indicated, e.g. the cortical gyri, the basal ganglia, details of the white matter, extracranial muscles and blood vessels, parts of the base and the vault of the skull, etc. The very precise topographical description of the numerous CT scan images was realized by the author by confrontation of these images with the corresponding anatomical sections of the same brain specimen, performed by an original technique.

  13. 33 CFR 165.T08-0432 - Safety Zone; Waterway Closure, Morgan City-Port Allen Route from Mile Marker 0 to Port Allen Lock.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Safety Zone; Waterway Closure, Morgan City-Port Allen Route from Mile Marker 0 to Port Allen Lock. 165.T08-0432 Section 165.T08-0432...-Port Allen Route from Mile Marker 0 to Port Allen Lock. (a) Location. Waters of the Gulf...

  14. Three-dimensional brain atlas of pygmy squid, Idiosepius paradoxus, revealing the largest relative vertical lobe system volume among the cephalopods.

    PubMed

    Koizumi, Motoki; Shigeno, Shuichi; Mizunami, Makoto; Tanaka, Nobuaki K

    2016-07-01

    Cephalopods have the largest and most complex nervous system of all invertebrates, and the brain-to-body weight ratio exceeds those of most fish and reptiles. The brain is composed of lobe units, the functions of which have been studied through surgical manipulation and electrical stimulation. However, how information is processed in each lobe for the animal to make a behavioral decision has rarely been investigated. To perform such functional analyses, it is necessary to precisely describe how brain lobes are spatially organized and mutually interconnected as a whole. We thus made three-dimensional digital brain atlases of both hatchling and juvenile pygmy squid, Idiosepius paradoxus. I. paradoxus is the smallest squid and has a brain small enough to scan as a whole region in the field-of-view of a low-magnification laser scan microscope objective. Precise analyses of the confocal images of the brains revealed one newly identified lobe and also that the relative volume of the vertical lobe system, the higher association center, in the pygmy squid represents the largest portion compared with the cephalopod species reported previously. In addition, principal component analyses of relative volumes of lobe complexes revealed that the organization of I. paradoxus brain is comparable to those of Decapodiformes species commonly used to analyze complex behaviors such as Sepia officinalis and Sepioteuthis sepioidea. These results suggest that the pygmy squid can be a good model to investigate the brain functions of coleoids utilizing physiological methods. J. Comp. Neurol. 524:2142-2157, 2016. © 2016 Wiley Periodicals, Inc. PMID:26663197

  15. Subcortical physiology deformed into a patient-specific brain atlas for image-guided stereotaxy

    NASA Astrophysics Data System (ADS)

    Finnis, Kirk; Starreveld, Yves P.; Parrent, Andrew; Peters, Terence M.

    2002-05-01

    Stereotactic neurosurgery for movement disorders involves the accurate localization of functionally distinct subcortical anatomy that appears homogeneous on magnetic resonance or computed tomographic images. To aid localization of these surgical targets on patient images, we have developed a visualization oriented searchable and expandable database of functional organization representing bilaterally the sensorimotor thalamus, pallidum, internal capsule, and subthalamic nucleus. Data were obtained through microelectrode recording and stimulation mapping routinely performed during 123 functional stereotactic procedures. Electrophysiologic data were standardized using a multi-parameter coding system and annotated to their respective MRIs at the appropriate position in patient stereotactic space. To accommodate for normal anatomical variability, we have developed an intensity-based nonlinear registration algorithm that rapidly warps a patient's volumetric MRI to a high-resolution MRI average brain. The annotated functional data are subsequently transformed into the average brain coordinate system using the displacement grids generated by the algorithm. When the database is searched, clustering of like inter-patient physiologic responses within target anatomy and adjacent structures is revealed. These data may in turn be registered to a preoperative MRI using a desktop computer enabling prior to surgery interactive delineation of surgical targets. The database is expandable, fully searchable, and provides a visual 3D representation of subcortical functional organization.

  16. SETI Surveys on the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Backus, Peter R.; Kilsdonk, T. N.; ATA Team

    2009-01-01

    The Allen Telescope Array (ATA-42) is a centimeter-wave array of 42 six-meter dishes that allows simultaneous SETI and other radio astronomy projects. In this paper we report on initial SETI observations using several observation and RFI mitigation strategies. We conducted both "targeted” observations of selected stars and "sky survey” observations of areas of the sky. Some observations were done with the SETI project directing the pointing of the array and others were "commensal,” in a direction selected by another project. In both modes, SETI observations used an independent RF tuning and two synthesized beams pointing at stars or positions in the field of view and tuned to the same frequency band. Results of the two SETI observations were compared and used to excise interference. In some observations, each beam had a null positioned at the center of the other beam. In the long term, we plan to observe one million target stars and survey large sections of the galactic plane over the frequency range from 1 GHz to 10 GHz. Much of this work may be done in parallel with other large-scale surveys. The first phase of the ATA was funded through generous grants from the Paul G. Allen Family Foundation. UC Berkeley, the SETI Institute, the National Science Foundation (Grant No. 0540599), Sun Microsystems, Xilinx, Nathan Myhrvold, Greg Papadopoulos, and other corporations and individual donors contributed additional funding.

  17. Macular pseudohaemorrhage secondary to Allen Dot artefact.

    PubMed

    Michaels, Luke; Alexander, Philip; Newsom, Richard

    2015-01-01

    A 34-year-old highly myopic (-11.00 D) woman presented to eye clinic with a 3 day history of right eye paracentral blurring. Visual acuities were 6/6 bilaterally. Clinical examination was normal. Fundus photography showed the classic appearance of a macular haemorrhage. This is a recognised complication of high myopia and would have accounted for the patient's symptoms. However, further photography showed that the haemorrhage seemed to 'jump' around the fundus and was even present in the fellow eye. The apparent haemorrhage was revealed to be an imaging artefact. The 'Allen Dot' is a 6 mm black mask incorporated into retinal cameras to reduce reflection. Rarely, in highly myopic eyes, optical artefact can result. To the best of our knowledge, we are the first in the literature to report artefacts from the Allen Dot masquerading as ophthalmic disease. This case re-iterates the importance of clinical examination, especially in high myopes, given the current trend towards virtual clinics. PMID:25564595

  18. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  19. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  20. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  1. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  2. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  3. Mission Specialist (MS) Allen experiments with beverage on middeck

    NASA Technical Reports Server (NTRS)

    1982-01-01

    Mission Specialist (MS) Allen, using beverage container and drinking straw, experiments with microgravity chararcteristics of orange juice on middeck in front of the Development Flight Instrument (DFI) unit and forward lockers. Allen laughes as he watches the results of his experimentation.

  4. Bi(OTf)3-catalyzed cycloisomerization of aryl-allenes.

    PubMed

    Lemière, Gilles; Cacciuttolo, Bastien; Belhassen, Emilie; Duñach, Elisabet

    2012-06-01

    Intramolecular hydroarylation of allenes was achieved under very mild conditions using bismuth(III) triflate as the catalyst. Efficient functionalization of activated and nonactivated aromatic nuclei led to C-C bond formation through a formal Ar-H activation. A tandem bis-hydroarylation of the allene moiety was also developed giving access to various interesting polycyclic structures. PMID:22578075

  5. Brain

    MedlinePlus

    ... will return after updating. Resources Archived Modules Updates Brain Cerebrum The cerebrum is the part of the ... the outside of the brain and spinal cord. Brain Stem The brain stem is the part of ...

  6. Identification of a set of genes showing regionally enriched expression in the mouse brain

    PubMed Central

    D'Souza, Cletus A; Chopra, Vikramjit; Varhol, Richard; Xie, Yuan-Yun; Bohacec, Slavita; Zhao, Yongjun; Lee, Lisa LC; Bilenky, Mikhail; Portales-Casamar, Elodie; He, An; Wasserman, Wyeth W; Goldowitz, Daniel; Marra, Marco A; Holt, Robert A; Simpson, Elizabeth M; Jones, Steven JM

    2008-01-01

    Background The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters (< 4 kb) that drive gene expression in specific brain regions or cell-types of therapeutic interest. Our goal was to first identify genes displaying regionally enriched expression in the mouse brain so that promoters designed from orthologous human genes can then be tested to drive reporter expression in a similar pattern in the mouse brain. Results We have utilized LongSAGE to identify regionally enriched transcripts in the adult mouse brain. As supplemental strategies, we also performed a meta-analysis of published literature and inspected the Allen Brain Atlas in situ hybridization data. From a set of approximately 30,000 mouse genes, 237 were identified as showing specific or enriched expression in 30 target regions of the mouse brain. GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology. Conclusion Using a multi-faceted expression validation approach, we have identified mouse genes whose human orthologs are good candidates for design of mini-promoters. These mouse genes represent molecular markers in several discrete brain regions/cell-types, which could potentially provide a mechanistic explanation of unique functions performed by each region. This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression. PMID:18625066

  7. Phase-transfer-catalysed asymmetric synthesis of tetrasubstituted allenes

    NASA Astrophysics Data System (ADS)

    Hashimoto, Takuya; Sakata, Kazuki; Tamakuni, Fumiko; Dutton, Mark J.; Maruoka, Keiji

    2013-03-01

    Allenes are molecules based on three carbons connected by two cumulated carbon-carbon double bonds. Given their axially chiral nature and unique reactivity, substituted allenes have a variety of applications in organic chemistry as key synthetic intermediates and directly as part of biologically active compounds. Although the demands for these motivated many endeavours to make axially chiral, substituted allenes by exercising asymmetric catalysis, the catalytic asymmetric synthesis of fully substituted ones (tetrasubstituted allenes) remained largely an unsolved issue. The fundamental obstacle to solving this conundrum is the lack of a simple synthetic transformation that provides tetrasubstituted allenes in the action of catalysis. We report herein a strategy to overcome this issue by the use of a phase-transfer-catalysed asymmetric functionalization of 1-alkylallene-1,3-dicarboxylates with N-arylsulfonyl imines and benzylic and allylic bromides.

  8. Freeman Allen: Boston's pioneering physician anesthetist.

    PubMed

    Morris, Samuel D; Morris, Alina J; Rockoff, Mark A

    2014-11-01

    On October 16, 1846 dentist William T. G. Morton successfully demonstrated at the Massachusetts General Hospital that ether could prevent the pain of surgery. For decades afterwards, the administration of anesthesia in the United States was generally relegated to dentists, medical students, junior surgical trainees, or even nonmedical personnel. It was not until the end of the 19th century that a few pioneering physicians began devoting their careers to administering anesthesia to patients, studying ways to make it safer and more effective, and teaching others about its use. One of these individuals was Freeman Allen, who was appointed the first physician anesthetist to the medical staff at the Massachusetts General Hospital and several other major hospitals in Boston. We describe this remarkable man, his contributions to the early development of anesthesiology as a medical specialty, and the true cause of his untimely death. PMID:25329027

  9. Neonatal Atlas Construction Using Sparse Representation

    PubMed Central

    Shi, Feng; Wang, Li; Wu, Guorong; Li, Gang; Gilmore, John H.; Lin, Weili; Shen, Dinggang

    2014-01-01

    Atlas construction generally includes first an image registration step to normalize all images into a common space and then an atlas building step to fuse the information from all the aligned images. Although numerous atlas construction studies have been performed to improve the accuracy of the image registration step, unweighted or simply weighted average is often used in the atlas building step. In this article, we propose a novel patch-based sparse representation method for atlas construction after all images have been registered into the common space. By taking advantage of local sparse representation, more anatomical details can be recovered in the built atlas. To make the anatomical structures spatially smooth in the atlas, the anatomical feature constraints on group structure of representations and also the overlapping of neighboring patches are imposed to ensure the anatomical consistency between neighboring patches. The proposed method has been applied to 73 neonatal MR images with poor spatial resolution and low tissue contrast, for constructing a neonatal brain atlas with sharp anatomical details. Experimental results demonstrate that the proposed method can significantly enhance the quality of the constructed atlas by discovering more anatomical details especially in the highly convoluted cortical regions. The resulting atlas demonstrates superior performance of our atlas when applied to spatially normalizing three different neonatal datasets, compared with other start-of-the-art neonatal brain atlases. PMID:24638883

  10. Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures.

    PubMed

    Lim, Issel Anne L; Faria, Andreia V; Li, Xu; Hsu, Johnny T C; Airan, Raag D; Mori, Susumu; van Zijl, Peter C M

    2013-11-15

    The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a "deep gray matter parcellation map" (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established "white matter parcellation map" (WMPM) from the same subject's T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the "Everything Parcellation Map in Eve Space," also known as the "EvePM." It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting "almost perfect" agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron concentrations in gray

  11. Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures.

    PubMed

    Lim, Issel Anne L; Faria, Andreia V; Li, Xu; Hsu, Johnny T C; Airan, Raag D; Mori, Susumu; van Zijl, Peter C M

    2013-11-15

    The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a "deep gray matter parcellation map" (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established "white matter parcellation map" (WMPM) from the same subject's T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the "Everything Parcellation Map in Eve Space," also known as the "EvePM." It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting "almost perfect" agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron concentrations in gray

  12. Sensitivity analysis and automation for intraoperative implementation of the atlas-based method for brain shift correction

    NASA Astrophysics Data System (ADS)

    Chen, Ishita; Simpson, Amber L.; Sun, Kay; Thompson, Reid C.; Miga, Michael I.

    2013-03-01

    The use of biomechanical models to correct the misregistration due to deformation in image guided neurosurgical systems has been a growing area of investigation. In previous work, an atlas-based inverse model was developed to account for soft-tissue deformations during image-guided surgery. Central to that methodology is a considerable amount of pre-computation and planning. The goal of this work is to evaluate techniques that could potentially reduce that burden. Distinct from previous manual techniques, an automated segmentation technique is described for the cerebrum and dural septa. The shift correction results using this automated segmentation method were compared to those using the manual methods. In addition, the extent and distribution of the surgical parameters associated with the deformation atlas were investigated by a sensitivity analysis using simulation experiments and clinical data. The shift correction results did not change significantly using the automated method (correction of 73+/-13% ) as compared to the semi-automated method from previous work (correction of 76+/-13%). The results of the sensitivity analysis show that the atlas could be constructed by coarser sampling (six fold reduction) without substantial degradation in the shift reconstruction, a decrease in preoperative computational time from 13.1+/-3.5 hours to 2.2+/-0.6 hours. The automated segmentation technique and the findings of the sensitivity study have significant impact on the reduction of pre-operative computational time, improving the utility of the atlas-based method. The work in this paper suggests that the atlas-based technique can become a `time of surgery' setup procedure rather than a pre-operative computing strategy.

  13. Segmentation of brain magnetic resonance images based on multi-atlas likelihood fusion: testing using data with a broad range of anatomical and photometric profiles

    PubMed Central

    Tang, Xiaoying; Crocetti, Deana; Kutten, Kwame; Ceritoglu, Can; Albert, Marilyn S.; Mori, Susumu; Mostofsky, Stewart H.; Miller, Michael I.

    2015-01-01

    We propose a hierarchical pipeline for skull-stripping and segmentation of anatomical structures of interest from T1-weighted images of the human brain. The pipeline is constructed based on a two-level Bayesian parameter estimation algorithm called multi-atlas likelihood fusion (MALF). In MALF, estimation of the parameter of interest is performed via maximum a posteriori estimation using the expectation-maximization (EM) algorithm. The likelihoods of multiple atlases are fused in the E-step while the optimal estimator, a single maximizer of the fused likelihoods, is then obtained in the M-step. There are two stages in the proposed pipeline; first the input T1-weighted image is automatically skull-stripped via a fast MALF, then internal brain structures of interest are automatically extracted using a regular MALF. We assess the performance of each of the two modules in the pipeline based on two sets of images with markedly different anatomical and photometric contrasts; 3T MPRAGE scans of pediatric subjects with developmental disorders vs. 1.5T SPGR scans of elderly subjects with dementia. Evaluation is performed quantitatively using the Dice overlap as well as qualitatively via visual inspections. As a result, we demonstrate subject-level differences in the performance of the proposed pipeline, which may be accounted for by age, diagnosis, or the imaging parameters (particularly the field strength). For the subcortical and ventricular structures of the two datasets, the hierarchical pipeline is capable of producing automated segmentations with Dice overlaps ranging from 0.8 to 0.964 when compared with the gold standard. Comparisons with other representative segmentation algorithms are presented, relative to which the proposed hierarchical pipeline demonstrates comparative or superior accuracy. PMID:25784852

  14. 2. Historic American Buildings Survey Harold Allen, Photographer 24 June ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. Historic American Buildings Survey Harold Allen, Photographer 24 June 1964 HALL AND MAIN STAIR, LOOKING NORTHWEST FROM ENTRANCE VESTIBULE - Edward E. Ayer House, 2 East Banks Street, Chicago, Cook County, IL

  15. 10. Historic American Buildings Survey Allen L. Hubbard, Photographer May ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. Historic American Buildings Survey Allen L. Hubbard, Photographer May 5, 1936 DINING ROOM 1ST FLOOR (west wall) - Holmes-Sayward House, West side of U.S. Route 202 (State Route 4), Alfred, York County, ME

  16. 9. Historic American Buildings Survey Allen L. Hubbard, Photographer May ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. Historic American Buildings Survey Allen L. Hubbard, Photographer May 5, 1936 NORTHEAST ROOM (1st floor south wall) - Holmes-Sayward House, West side of U.S. Route 202 (State Route 4), Alfred, York County, ME

  17. 8. Historic American Buildings Survey Allen L. Hubbard, Photographer May ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Historic American Buildings Survey Allen L. Hubbard, Photographer May 5, 1936 NORTHEAST ROOM (west wall) - Holmes-Sayward House, West side of U.S. Route 202 (State Route 4), Alfred, York County, ME

  18. 6. Historic American Buildings Survey Harold Allen, Photographer June 1964 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. Historic American Buildings Survey Harold Allen, Photographer June 1964 STAINED GLASS WINDOW, WEST WINDOW IN SOUTH WALL, FROM BALCONY - Kehilath Anshe Ma'ariv Synagogue, 3301 South Indiana Avenue, Chicago, Cook County, IL

  19. 8. Historic American Buildings Survey Harold Allen, Photographer 24 June ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Historic American Buildings Survey Harold Allen, Photographer 24 June 1964 GRAND STAIRWAY, FROM SECOND FLOOR HALL, SHOWING STAINED GLASS WINDOW IN WEST WALL ABOVE LANDING - Francis J. Dewes House, 503 West Wrightwood Avenue, Chicago, Cook County, IL

  20. 3. Historic American Buildings Survey Harold Allen, Photographer 3 May ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. Historic American Buildings Survey Harold Allen, Photographer 3 May 1965 ENTRANCE CANOPY FROM SOUTHWEST - Holy Trinity Russian & Greek Orthodox Church, 1121 North Leavitt Street, Chicago, Cook County, IL

  1. 1. Historic American Buildings Survey Harold Allen, Photographer 31 May ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Historic American Buildings Survey Harold Allen, Photographer 31 May 1964 WEST (NORMAL AVE.) AND SOUTHEAST (CANALPORT AVE.) ELEVATIONS - Schoenhofen Brewing Company, Powerhouse, 1770 Canalport Avenue, Chicago, Cook County, IL

  2. Synthesis and biological evaluation of 12 allenic aromatic ethers.

    PubMed

    Wang, San-Yong; Mao, Wei-Wei; She, Zhi-Gang; Li, Chun-Rong; Yang, Ding-Qiao; Lin, Yong-Cheng; Fu, Li-Wu

    2007-05-15

    Twelve allenic aromatic ethers, some of them are natural products isolated from the mangrove fungus Xylaria sp. 2508 in the South China Sea, were synthesized. Their antitumor activities against KB and KBv200 cells were determined. All these compounds demonstrated cytotoxic potential, ranging from weak to strong activity. The analysis of structure-activity relationships suggested that the introduction of allenic moiety could generate or enhance cytotoxicity of these phenol compounds.

  3. Voices: A Conversation with Allen J. Wilcox.

    PubMed

    Jukic, Anne Marie Z

    2016-09-01

    Allen James Wilcox was born on 30 September 1946 in Columbus, OH. He studied medicine at the University of Michigan, graduated in 1973, and after a rotating internship, he completed a master's degree in maternal and child health (1976) and a PhD in epidemiology (1979) at the University of North Carolina in Chapel Hill. After graduation, he went to work at the National Institute of Environmental Health Sciences (NIEHS, one of the US National Institutes of Health) in Durham, NC, where he has spent his career. He developed a research program in reproductive and perinatal epidemiology, a relatively unexplored area at the time. His studies include the early pregnancy study, which documented the extent of subclinical pregnancy loss in humans and established the fertile days of a woman's menstrual cycle. He served as the Chief of the Epidemiology Branch from 1991 to 2001, and as Editor-in-Chief of the journal EPIDEMIOLOGY from 2001 to 2014. His textbook, Fertility and Pregnancy-An Epidemiologic Perspective, was published by Oxford University Press in 2010. He was elected to the American Epidemiological Society in 1989, and served as its president in 2003. He also served as president of the Society of Pediatric and Perinatal Epidemiological Research (1996) and the president of the Society of Epidemiological Research (1998). He holds adjunct teaching appointments at the University of North Carolina, Harvard University, and the University of Bergen (Norway), which awarded him an honorary doctoral degree in 2008. PMID:27482869

  4. Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain.

    PubMed

    Ng, Lydia; Pathak, Sayan D; Kuan, Chihchau; Lau, Chris; Dong, Hongwei; Sodt, Andrew; Dang, Chinh; Avants, Brian; Yushkevich, Paul; Gee, James C; Haynor, David; Lein, Ed; Jones, Allan; Hawrylycz, Mike

    2007-01-01

    Large scale gene expression studies in the mammalian brain offer the promise of understanding the topology, networks and ultimately the function of its complex anatomy, opening previously unexplored avenues in neuroscience. High-throughput methods permit genome-wide searches to discover genes that are uniquely expressed in brain circuits and regions that control behavior. Previous gene expression mapping studies in model organisms have employed situ hybridization (ISH), a technique that uses labeled nucleic acid probes to bind to specific mRNA transcripts in tissue sections. A key requirement for this effort is the development of fast and robust algorithms for anatomically mapping and quantifying gene expression for ISH. We describe a neuroinformatics pipeline for automatically mapping expression profiles of ISH data and its use to produce the first genomic scale 3-D mapping of gene expression in a mammalian brain. The pipeline is fully automated and adaptable to other organisms and tissues. Our automated study of over 20,000 genes indicates that at least 78.8 percent are expressed at some level in the adult C56BL/6J mouse brain. In addition to providing a platform for genomic scale search, high-resolution images and visualization tools for expression analysis are available at the Allen Brain Atlas web site (http://www.brain-map.org).

  5. Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain

    PubMed Central

    Chou, Shen-Ju; Wang, Chindi; Sintupisut, Nardnisa; Niou, Zhen-Xian; Lin, Chih-Hsu; Li, Ker-Chau; Yeang, Chen-Hsiang

    2016-01-01

    Allen Brain Atlas (ABA) provides a valuable resource of spatial/temporal gene expressions in mammalian brains. Despite rich information extracted from this database, current analyses suffer from several limitations. First, most studies are either gene-centric or region-centric, thus are inadequate to capture the superposition of multiple spatial-temporal patterns. Second, standard tools of expression analysis such as matrix factorization can capture those patterns but do not explicitly incorporate spatial dependency. To overcome those limitations, we proposed a computational method to detect recurrent patterns in the spatial-temporal gene expression data of developing mouse brains. We demonstrated that regional distinction in brain development could be revealed by localized gene expression patterns. The patterns expressed in the forebrain, medullary and pontomedullary, and basal ganglia are enriched with genes involved in forebrain development, locomotory behavior, and dopamine metabolism respectively. In addition, the timing of global gene expression patterns reflects the general trends of molecular events in mouse brain development. Furthermore, we validated functional implications of the inferred patterns by showing genes sharing similar spatial-temporal expression patterns with Lhx2 exhibited differential expression in the embryonic forebrains of Lhx2 mutant mice. These analysis outcomes confirm the utility of recurrent expression patterns in studying brain development. PMID:26786896

  6. Common Genetic Variant in VIT Is Associated with Human Brain Asymmetry

    PubMed Central

    Tadayon, Sayed H.; Vaziri-Pashkam, Maryam; Kahali, Pegah; Ansari Dezfouli, Mitra; Abbassian, Abdolhossein

    2016-01-01

    Brain asymmetry varies across individuals. However, genetic factors contributing to this normal variation are largely unknown. Here we studied variation of cortical surface area asymmetry in a large sample of subjects. We performed principal component analysis (PCA) to capture correlated asymmetry variation across cortical regions. We found that caudal and rostral anterior cingulate together account for a substantial part of asymmetry variation among individuals. To find SNPs associated with this subset of brain asymmetry variation we performed a genome-wide association study followed by replication in an independent cohort. We identified one SNP (rs11691187) that had genome-wide significant association (PCombined = 2.40e-08). The rs11691187 is in the first intron of VIT. In a follow-up analysis, we found that VIT gene expression is associated with brain asymmetry in six donors of the Allen Human Brain Atlas. Based on these findings we suggest that VIT contributes to normal brain asymmetry variation. Our results can shed light on disorders associated with altered brain asymmetry. PMID:27252636

  7. Quantification of Tc-99m-ethyl cysteinate dimer brain single photon emission computed tomography images using statistical probabilistic brain atlas in depressive end-stage renal disease patients

    PubMed Central

    Kim, Heeyoung; Kim, In Joo; Kim, Seong-Jang; Song, Sang Heon; Pak, Kyoungjune; Kim, Keunyoung

    2012-01-01

    This study adapted a statistical probabilistic anatomical map of the brain for single photon emission computed tomography images of depressive end-stage renal disease patients. This research aimed to investigate the relationship between symptom clusters, disease severity, and cerebral blood flow. Twenty-seven patients (16 males, 11 females) with stages 4 and 5 end-stage renal disease were enrolled, along with 25 healthy controls. All patients underwent depressive mood assessment and brain single photon emission computed tomography. The statistical probabilistic anatomical map images were used to calculate the brain single photon emission computed tomography counts. Asymmetric index was acquired and Pearson correlation analysis was performed to analyze the correlation between symptom factors, severity, and regional cerebral blood flow. The depression factors of the Hamilton Depression Rating Scale showed a negative correlation with cerebral blood flow in the left amygdale. The insomnia factor showed negative correlations with cerebral blood flow in the left amygdala, right superior frontal gyrus, right middle frontal gyrus, and left middle frontal gyrus. The anxiety factor showed a positive correlation with cerebral glucose metabolism in the cerebellar vermis and a negative correlation with cerebral glucose metabolism in the left globus pallidus, right inferior frontal gyrus, both temporal poles, and left parahippocampus. The overall depression severity (total scores of Hamilton Depression Rating Scale) was negatively correlated with the statistical probabilistic anatomical map results in the left amygdala and right inferior frontal gyrus. In conclusion, our results demonstrated that the disease severity and extent of cerebral blood flow quantified by a probabilistic brain atlas was related to various brain areas in terms of the overall severity and symptom factors in end-stage renal disease patients. PMID:25558229

  8. Reactivity and Chemoselectivity of Allenes in Rh(I)-Catalyzed Intermolecular (5 + 2) Cycloadditions with Vinylcyclopropanes: Allene-Mediated Rhodacycle Formation Can Poison Rh(I)-Catalyzed Cycloadditions

    PubMed Central

    2015-01-01

    Allenes are important 2π building blocks in organic synthesis and engage as 2-carbon components in many metal-catalyzed reactions. Wender and co-workers discovered that methyl substituents on the terminal allene double bond counterintuitively change the reactivities of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with vinylcyclopropanes (VCPs). More sterically encumbered allenes afford higher cycloadduct yields, and such effects are also observed in other Rh(I)-catalyzed intermolecular cycloadditions. Through density functional theory calculations (B3LYP and M06) and experiment, we explored this enigmatic reactivity and selectivity of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with VCPs. The apparent low reactivity of terminally unsubstituted allenes is associated with a competing allene dimerization that irreversibly sequesters rhodium. With terminally substituted allenes, steric repulsion between the terminal substituents significantly increases the barrier of allene dimerization while the barrier of the (5 + 2) cycloaddition is not affected, and thus the cycloaddition prevails. Computation has also revealed the origin of chemoselectivity in (5 + 2) cycloadditions with allene-ynes. Although simple allene and acetylene have similar reaction barriers, intermolecular (5 + 2) cycloadditions of allene-ynes occur exclusively at the terminal allene double bond. The terminal double bond is more reactive due to the enhanced d−π* backdonation. At the same time, insertion of the internal double bond of an allene-yne has a higher barrier as it would break π conjugation. Substituted alkynes are more difficult to insert compared with acetylene, because of the steric repulsion from the additional substituents. This leads to the greater reactivity of the allene double bond relative to the alkynyl group in allene-ynes. PMID:25379606

  9. Reactivity and chemoselectivity of allenes in Rh(I)-catalyzed intermolecular (5 + 2) cycloadditions with vinylcyclopropanes: allene-mediated rhodacycle formation can poison Rh(I)-catalyzed cycloadditions.

    PubMed

    Hong, Xin; Stevens, Matthew C; Liu, Peng; Wender, Paul A; Houk, K N

    2014-12-10

    Allenes are important 2π building blocks in organic synthesis and engage as 2-carbon components in many metal-catalyzed reactions. Wender and co-workers discovered that methyl substituents on the terminal allene double bond counterintuitively change the reactivities of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with vinylcyclopropanes (VCPs). More sterically encumbered allenes afford higher cycloadduct yields, and such effects are also observed in other Rh(I)-catalyzed intermolecular cycloadditions. Through density functional theory calculations (B3LYP and M06) and experiment, we explored this enigmatic reactivity and selectivity of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with VCPs. The apparent low reactivity of terminally unsubstituted allenes is associated with a competing allene dimerization that irreversibly sequesters rhodium. With terminally substituted allenes, steric repulsion between the terminal substituents significantly increases the barrier of allene dimerization while the barrier of the (5 + 2) cycloaddition is not affected, and thus the cycloaddition prevails. Computation has also revealed the origin of chemoselectivity in (5 + 2) cycloadditions with allene-ynes. Although simple allene and acetylene have similar reaction barriers, intermolecular (5 + 2) cycloadditions of allene-ynes occur exclusively at the terminal allene double bond. The terminal double bond is more reactive due to the enhanced d-π* backdonation. At the same time, insertion of the internal double bond of an allene-yne has a higher barrier as it would break π conjugation. Substituted alkynes are more difficult to insert compared with acetylene, because of the steric repulsion from the additional substituents. This leads to the greater reactivity of the allene double bond relative to the alkynyl group in allene-ynes.

  10. Obituary: James Alfred Van Allen, 1914-2006

    NASA Astrophysics Data System (ADS)

    Ludwig, George H.; McIlwain, Carl Edwin

    2006-12-01

    James Alfred Van Allen, world-renowned space scientist, died 9 August 2006 at the age of ninety-one. He succumbed to heart failure after a ten-week period of declining health. Van Allen served for his entire sixty-seven-year professional career as an amazingly productive researcher, space science spokesman, inspired teacher, and valued colleague. The realization by him and his associates that charged particles are trapped by the Earth's magnetic field began a whole new field of research, magnetospheric physics. Following that initial discovery, he and his associates quickly extended their observations, first to the inner planets, and then to the rest of the planets and beyond. During his tenure at Iowa, he and his group flew instruments on more than sixty successful Earth satellites and planetary spacecraft, including the first missions to the planets Venus, Mars, Jupiter, Saturn, Uranus, and Neptune. Van Allen's lifetime publication list numbers more than 275, of which many are widely-cited, seminal papers. He was the sole author of more than 125 of those papers. Beyond the research laboratory, Van Allen worked energetically throughout his career in establishing space research as a new branch of human inquiry. He was among the most sought-after as a committee member and adviser, working at the highest levels of government, including the White House and Congress, and at all levels of the national and international research establishments. Many presentations in the non-scientific arena helped to bring the exciting discoveries and challenges of space research to the attention of the general public. James Van Allen (Van to his many friends and colleagues) was born on 7 September 1914 on a small farm near Mount Pleasant, Iowa, the second of four sons of Alfred Morris Van Allen and Alma Olney Van Allen. After high school in Mount Pleasant, he entered Iowa Wesleyan College, majoring in physics and graduating summa cum laude. While there, he was introduced to geophysics

  11. Atlas-based system for functional neurosurgery

    NASA Astrophysics Data System (ADS)

    Nowinski, Wieslaw L.; Yeo, Tseng T.; Yang, Guo L.; Dow, Douglas E.

    1997-05-01

    This paper addresses the development of an atlas-based system for preoperative functional neurosurgery planning and training, intraoperative support and postoperative analysis. The system is based on Atlas of Stereotaxy of the Human Brain by Schaltenbrand and Wahren used for interactive segmentation and labeling of clinical data in 2D/3D, and for assisting stereotactic targeting. The atlas microseries are digitized, enhanced, segmented, labeled, aligned and organized into mutually preregistered atlas volumes 3D models of the structures are also constructed. The atlas may be interactively registered with the actual patient's data. Several other features are also provided including data reformatting, visualization, navigation, mensuration, and stereotactic path display and editing in 2D/3D. The system increases the accuracy of target definition, reduces the time of planning and time of the procedure itself. It also constitutes a research platform for the construction of more advanced neurosurgery supporting tools and brain atlases.

  12. Reply to David Kemmerer's "a critique of Mark D. Allen's 'the preservation of verb subcategory knowledge in a spoken language comprehension deficit'".

    PubMed

    Allen, Mark D; Owens, Tyler E

    2008-07-01

    Allen [Allen, M. D. (2005). The preservation of verb subcategory knowledge in a spoken language comprehension deficit. Brain and Language, 95, 255-264] presents evidence from a single patient, WBN, to motivate a theory of lexical processing and representation in which syntactic information may be encoded and retrieved independently of semantic information. In his critique, Kemmerer argues that because Allen depended entirely on preposition-based verb subcategory violations to test WBN's knowledge of correct argument structure, his results, at best, address a "strawman" theory. This argument rests on the assumption that preposition subcategory options are superficial syntactic phenomena which are not represented by argument structure proper. We demonstrate that preposition subcategory is in fact treated as semantically determined argument structure in the theories that Allen evaluated, and thus far from irrelevant. In further discussion of grammatically relevant versus irrelevant semantic features, Kemmerer offers a review of his own studies. However, due to an important design shortcoming in these experiments, we remain unconvinced. Reemphasizing the fact the Allen (2005) never claimed to rule out all semantic contributions to syntax, we propose an improvement in Kemmerer's approach that might provide more satisfactory evidence on the distinction between the kinds of relevant versus irrelevant features his studies have addressed.

  13. Exploiting [2+2] cycloaddition chemistry: achievements with allenes.

    PubMed

    Alcaide, Benito; Almendros, Pedro; Aragoncillo, Cristina

    2010-02-01

    The allene moiety represents an excellent partner for the [2+2] cycloaddition with alkenes and alkynes, affording the cyclobutane and cyclobutene skeletons in a single step. This strategy has been widely studied under thermal, photochemical and microwave induced conditions. More recently, the use of transition metal catalysis has been introduced as an alternative relying on the activation of the allenic component. On the other hand, the intramolecular version has attracted much attention as a strategy for the synthesis of polycyclic compounds in a regio- and stereoselective fashion. This critical review focuses on the most recently developed [2+2] cycloadditions on allenes along with remarkable early works accounting for the mechanism, the regio- and diastereoselectivity of the cycloadducts formed (103 references).

  14. 5. Historic American Buildings Survey Harold Allen, Photographer June 1964 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Historic American Buildings Survey Harold Allen, Photographer June 1964 TRIPLE STAINED GLASS WINDOWS AND COLUMN SUPPORTING BALCONY (EAST WINDOWS IN SOUTH WALL OF MAIN FLOOR OF AUDITORIUM) - Kehilath Anshe Ma'ariv Synagogue, 3301 South Indiana Avenue, Chicago, Cook County, IL

  15. Van Allen Probes Science Gateway: A Centralized Data Access Point

    NASA Astrophysics Data System (ADS)

    Romeo, G.; Barnes, R. J.; Ukhorskiy, A. Y.; Sotirelis, T.; Stephens, G. K.; Kessel, R.; Potter, M.

    2015-12-01

    The Van Allen Probes Science Gateway acts a centralized interface to the instrument Science Operation Centers (SOCs), provides mission planning tools, and hosts a number of science related activities such as the mission bibliography. Most importantly, the Gateway acts as the primary site for processing and delivering the Van Allen Probes Space Weather data to users. Over the past years, the web-site has been completely redesigned with the focus on easier navigation and improvements of the existing tools such as the orbit plotter, position calculator and magnetic footprint tool. In addition, a new data plotting facility has been added. Based on HTML5, which allows users to interactively plot Van Allen Probes science and space weather data. The user can tailor the tool to display exactly the plot they wish to see and then share this with other users via either a URL or by QR code. Various types of plots can be created, including, simple time series, data plotted as a function of orbital location, and time versus L-Shell, capability of visualizing data from both probes (A & B) on the same plot. In cooperation with all Van Allen Probes Instrument SOCs, the Science Gateway will soon be able to serve higher level data products (Level 3), and to visualize them via the above mentioned HTML5 interface. Users will also be able to create customized CDF files on the fly.

  16. 18. VIEW SHOWING, LEFT TO RIGHT, H. J. LAWSON, ALLEN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. VIEW SHOWING, LEFT TO RIGHT, H. J. LAWSON, ALLEN MATTISON, SENATOR CARL HAYDEN, LIN B. ORME, PAUL ROCA, AND J. A. FRAPS. THE UPSTREAM FACE AND SPILLWAY GATES ARE VISIBLE IN THE BACKGROUND. October 1938 - Bartlett Dam, Verde River, Phoenix, Maricopa County, AZ

  17. James Van Allen and His Namesake NASA Mission

    NASA Astrophysics Data System (ADS)

    Baker, D. N.; Hoxie, V. C.; Jaynes, A.; Kale, A.; Kanekal, S. G.; Li, X.; Reeves, G. D.; Spence, H. E.

    2013-12-01

    In many ways, James A. Van Allen defined and "invented" modern space research. His example showed the way for government-university partners to pursue basic research that also served important national and international goals. He was a tireless advocate for space exploration and for the role of space science in the spectrum of national priorities.

  18. Regioselective intramolecular [3+2] annulation of allene-nitrones.

    PubMed

    Inagaki, Fuyuhiko; Kobayashi, Harumi; Mukai, Chisato

    2012-01-01

    The regioselective intramolecular 1,3-dipolar cycloaddition of the phenylsulfonylallene-nitrone derivatives has been developed. This reaction showed that the distal double bond of the allene exclusively reacted with the nitrone group to produce the bicyclic isoxazolidine derivatives regardless of the substitution pattern on the allenyl moiety.

  19. Thermal induced intramolecular [2 + 2] cycloaddition of allene-ACPs.

    PubMed

    Chen, Kai; Sun, Run; Xu, Qin; Wei, Yin; Shi, Min

    2013-06-28

    A facile synthetic method for preparation of bicyclo[4.2.0] nitrogen heterocycles has been developed via a thermal induced intramolecular [2 + 2] cycloaddition reaction of allene-ACPs. The DFT calculations indicate that this intramolecular cycloaddition proceeds in a concerted manner and a strained small ring is essential.

  20. The Evolving Space Weather System—Van Allen Probes Contribution

    NASA Astrophysics Data System (ADS)

    Zanetti, L. J.; Mauk, B. H.; Fox, N. J.; Barnes, R. J.; Weiss, M.; Sotirelis, T. S.; Raouafi, N.-E.; Kessel, R. L.; Becker, H. N.

    2014-10-01

    The overarching goal and purpose of the study of space weather is clear—to understand and address the issues caused by solar disturbances on humans and technological systems. Space weather has evolved in the past few decades from a collection of concerned agencies and researchers to a critical function of the National Weather Service of NOAA. The general effects have also evolved from the well-known telegraph disruptions of the mid-1800s to modern day disturbances of the electric power grid, communications and navigation, human spaceflight and spacecraft systems. The last two items in this list, and specifically the effects of penetrating radiation, were the impetus for the space weather broadcast implemented on NASA's Van Allen Probes' twin pair of satellites, launched in August of 2012 and orbiting directly through Earth's severe radiation belts. The Van Allen Probes mission, formerly the Radiation Belt Storm Probes (RBSP), was renamed soon after launch to honor the discoverer of Earth's radiation belts at the beginning of the space age, the late James Van Allen (the spacecraft themselves are still referred to as RBSP-A and RBSP-B). The Van Allen Probes are one part of NASA's Living With a Star program formulated to advance the scientific understanding of the connection between solar disturbances, the resulting heliospheric conditions, and their effects on the geospace and Earth environment.

  1. A stereotaxic, population-averaged T1w ovine brain atlas including cerebral morphology and tissue volumes

    PubMed Central

    Nitzsche, Björn; Frey, Stephen; Collins, Louis D.; Seeger, Johannes; Lobsien, Donald; Dreyer, Antje; Kirsten, Holger; Stoffel, Michael H.; Fonov, Vladimir S.; Boltze, Johannes

    2015-01-01

    Standard stereotaxic reference systems play a key role in human brain studies. Stereotaxic coordinate systems have also been developed for experimental animals including non-human primates, dogs, and rodents. However, they are lacking for other species being relevant in experimental neuroscience including sheep. Here, we present a spatial, unbiased ovine brain template with tissue probability maps (TPM) that offer a detailed stereotaxic reference frame for anatomical features and localization of brain areas, thereby enabling inter-individual and cross-study comparability. Three-dimensional data sets from healthy adult Merino sheep (Ovis orientalis aries, 12 ewes and 26 neutered rams) were acquired on a 1.5 T Philips MRI using a T1w sequence. Data were averaged by linear and non-linear registration algorithms. Moreover, animals were subjected to detailed brain volume analysis including examinations with respect to body weight (BW), age, and sex. The created T1w brain template provides an appropriate population-averaged ovine brain anatomy in a spatial standard coordinate system. Additionally, TPM for gray (GM) and white (WM) matter as well as cerebrospinal fluid (CSF) classification enabled automatic prior-based tissue segmentation using statistical parametric mapping (SPM). Overall, a positive correlation of GM volume and BW explained about 15% of the variance of GM while a positive correlation between WM and age was found. Absolute tissue volume differences were not detected, indeed ewes showed significantly more GM per bodyweight as compared to neutered rams. The created framework including spatial brain template and TPM represent a useful tool for unbiased automatic image preprocessing and morphological characterization in sheep. Therefore, the reported results may serve as a starting point for further experimental and/or translational research aiming at in vivo analysis in this species. PMID:26089780

  2. Propargyltrimethylsilanes as allene equivalents in transition metal-catalyzed [5 + 2] cycloadditions.

    PubMed

    Wender, Paul A; Inagaki, Fuyuhiko; Pfaffenbach, Magnus; Stevens, Matthew C

    2014-06-01

    Conventional allenes have not been effective π-reactive 2-carbon components in many intermolecular cycloadditions including metal-catalyzed [5 + 2] cycloadditions. We report herein that rhodium-catalyzed [5 + 2] cycloadditions of propargyltrimethylsilanes and vinylcyclopropanes provide, after in situ protodesilylation, a highly efficient route to formal allene cycloadducts. Propargyltrimethylsilanes function as safe, easily handled synthetic equivalents of gaseous allenes and hard-to-access monosubstituted allenes. In this one-flask procedure, they provide cycloadducts of what is formally addition to the more sterically encumbered allene double bond.

  3. Propargyltrimethylsilanes as Allene Equivalents in Transition Metal-Catalyzed [5 + 2] Cycloadditions

    PubMed Central

    2015-01-01

    Conventional allenes have not been effective π-reactive 2-carbon components in many intermolecular cycloadditions including metal-catalyzed [5 + 2] cycloadditions. We report herein that rhodium-catalyzed [5 + 2] cycloadditions of propargyltrimethylsilanes and vinylcyclopropanes provide, after in situ protodesilylation, a highly efficient route to formal allene cycloadducts. Propargyltrimethylsilanes function as safe, easily handled synthetic equivalents of gaseous allenes and hard-to-access monosubstituted allenes. In this one-flask procedure, they provide cycloadducts of what is formally addition to the more sterically encumbered allene double bond. PMID:24819093

  4. Evaluation of Atlas-Based White Matter Segmentation with Eve

    PubMed Central

    Plassard, Andrew J.; Hinton, Kendra E.; Venkatraman, Vijay; Gonzalez, Christopher; Resnick, Susan M.; Landman, Bennett A.

    2015-01-01

    Multi-atlas labeling has come in wide spread use for whole brain labeling on magnetic resonance imaging. Recent challenges have shown that leading techniques are near (or at) human expert reproducibility for cortical gray matter labels. However, these approaches tend to treat white matter as essentially homogeneous (as white matter exhibits isointense signal on structural MRI). The state-of-the-art for white matter atlas is the single-subject Johns Hopkins Eve atlas. Numerous approaches have attempted to use tractography and/or orientation information to identify homologous white matter structures across subjects. Despite success with large tracts, these approaches have been plagued by difficulties in with subtle differences in course, low signal to noise, and complex structural relationships for smaller tracts. Here, we investigate use of atlas-based labeling to propagate the Eve atlas to unlabeled datasets. We evaluate single atlas labeling and multi-atlas labeling using synthetic atlases derived from the single manually labeled atlas. On 5 representative tracts for 10 subjects, we demonstrate that (1) single atlas labeling generally provides segmentations within 2mm mean surface distance, (2) morphologically constraining DTI labels within structural MRI white matter reduces variability, and (3) multi-atlas labeling did not improve accuracy. These efforts present a preliminary indication that single atlas labels with correction is reasonable, but caution should be applied. To purse multi-atlas labeling and more fully characterize overall performance, more labeled datasets would be necessary. PMID:25914503

  5. Obituary: James Alfred Van Allen, 1914-2006

    NASA Astrophysics Data System (ADS)

    Ludwig, George H.; McIlwain, Carl Edwin

    2006-12-01

    James Alfred Van Allen, world-renowned space scientist, died 9 August 2006 at the age of ninety-one. He succumbed to heart failure after a ten-week period of declining health. Van Allen served for his entire sixty-seven-year professional career as an amazingly productive researcher, space science spokesman, inspired teacher, and valued colleague. The realization by him and his associates that charged particles are trapped by the Earth's magnetic field began a whole new field of research, magnetospheric physics. Following that initial discovery, he and his associates quickly extended their observations, first to the inner planets, and then to the rest of the planets and beyond. During his tenure at Iowa, he and his group flew instruments on more than sixty successful Earth satellites and planetary spacecraft, including the first missions to the planets Venus, Mars, Jupiter, Saturn, Uranus, and Neptune. Van Allen's lifetime publication list numbers more than 275, of which many are widely-cited, seminal papers. He was the sole author of more than 125 of those papers. Beyond the research laboratory, Van Allen worked energetically throughout his career in establishing space research as a new branch of human inquiry. He was among the most sought-after as a committee member and adviser, working at the highest levels of government, including the White House and Congress, and at all levels of the national and international research establishments. Many presentations in the non-scientific arena helped to bring the exciting discoveries and challenges of space research to the attention of the general public. James Van Allen (Van to his many friends and colleagues) was born on 7 September 1914 on a small farm near Mount Pleasant, Iowa, the second of four sons of Alfred Morris Van Allen and Alma Olney Van Allen. After high school in Mount Pleasant, he entered Iowa Wesleyan College, majoring in physics and graduating summa cum laude. While there, he was introduced to geophysics

  6. Van Allen Probes: Resolving Fundamental Physics with Practical Consequences

    NASA Astrophysics Data System (ADS)

    Ukhorskiy, Aleksandr; Sibeck, David; Fox, Nicola; Mauk, Barry; Kessel, Ramona

    The Van Allen Probes twin spacecraft were launched on 30 August 2012 into nearly identical, 1.1 x 5.8 Re elliptical, low inclination (10°) Earth orbits with one of the two spacecraft lapping the other about every 2.5 months. The goal of the mission is to provide understanding of how populations of relativistic electrons and penetrating ions in space form or change in response to variable inputs of energy from the Sun. In this paper we overview the new understanding and discoveries of the Van Allen Probes science investigations since the operational mission began on 1 November 2012, which include formation of multiple coherently ordered structures within the outer electron belt and new persistent “zebra stripes” in the inner electron belt.

  7. Isomer-specific combustion chemistry in allene and propyne flames

    SciTech Connect

    Hansen, Nils; Miller, James A.; Westmoreland, Phillip R.; Kasper, Tina; Kohse-Hoeinghaus, Katharina; Wang, Juan; Cool, Terrill A.

    2009-11-15

    A combined experimental and modeling study is performed to clarify the isomer-specific combustion chemistry in flames fueled by the C{sub 3}H{sub 4} isomers allene and propyne. To this end, mole fraction profiles of several flame species in stoichiometric allene (propyne)/O{sub 2}/Ar flames are analyzed by means of a chemical kinetic model. The premixed flames are stabilized on a flat-flame burner under a reduced pressure of 25 Torr (=33.3 mbar). Quantitative species profiles are determined by flame-sampling molecular-beam mass spectrometry, and the isomer-specific flame compositions are unraveled by employing photoionization with tunable vacuum-ultraviolet synchrotron radiation. The temperature profiles are measured by OH laser-induced fluorescence. Experimental and modeled mole fraction profiles of selected flame species are discussed with respect to the isomer-specific combustion chemistry in both flames. The emphasis is put on main reaction pathways of fuel consumption, of allene and propyne isomerization, and of isomer-specific formation of C{sub 6} aromatic species. The present model includes the latest theoretical rate coefficients for reactions on a C{sub 3}H{sub 5} potential [J.A. Miller, J.P. Senosiain, S.J. Klippenstein, Y. Georgievskii, J. Phys. Chem. A 112 (2008) 9429-9438] and for the propargyl recombination reactions [Y. Georgievskii, S.J. Klippenstein, J.A. Miller, Phys. Chem. Chem. Phys. 9 (2007) 4259-4268]. Larger peak mole fractions of propargyl, allyl, and benzene are observed in the allene flame than in the propyne flame. In these flames virtually all of the benzene is formed by the propargyl recombination reaction. (author)

  8. Van Allen Probes Science Gateway and Space Weather Data Processing

    NASA Astrophysics Data System (ADS)

    Romeo, G.; Barnes, R. J.; Weiss, M.; Fox, N. J.; Mauk, B.; Potter, M.; Kessel, R.

    2014-12-01

    The Van Allen Probes Science Gateway acts as a centralized interface to the instrument Science Operation Centers (SOCs), provides mission planning tools, and hosts a number of science related activities such as the mission bibliography. Most importantly, the Gateway acts as the primary site for processing and delivering the VAP Space Weather data to users. Over the past year, the web-site has been completely redesigned with the focus on easier navigation and improvements of the existing tools such as the orbit plotter, position calculator and magnetic footprint tool. In addition, a new data plotting facility has been added. Based on HTML5, which allows users to interactively plot Van Allen Probes summary and space weather data. The user can tailor the tool to display exactly the plot they wish to see and then share this with other users via either a URL or by QR code. Various types of plots can be created, including simple time series, data plotted as a function of orbital location, and time versus L-Shell. We discuss the new Van Allen Probes Science Gateway and the Space Weather Data Pipeline.

  9. Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain.

    PubMed

    Ko, Younhee; Ament, Seth A; Eddy, James A; Caballero, Juan; Earls, John C; Hood, Leroy; Price, Nathan D

    2013-02-19

    To characterize gene expression patterns in the regional subdivisions of the mammalian brain, we integrated spatial gene expression patterns from the Allen Brain Atlas for the adult mouse with panels of cell type-specific genes for neurons, astrocytes, and oligodendrocytes from previously published transcriptome profiling experiments. We found that the combined spatial expression patterns of 170 neuron-specific transcripts revealed strikingly clear and symmetrical signatures for most of the brain's major subdivisions. Moreover, the brain expression spatial signatures correspond to anatomical structures and may even reflect developmental ontogeny. Spatial expression profiles of astrocyte- and oligodendrocyte-specific genes also revealed regional differences; these defined fewer regions and were less distinct but still symmetrical in the coronal plane. Follow-up analysis suggested that region-based clustering of neuron-specific genes was related to (i) a combination of individual genes with restricted expression patterns, (ii) region-specific differences in the relative expression of functional groups of genes, and (iii) regional differences in neuronal density. Products from some of these neuron-specific genes are present in peripheral blood, raising the possibility that they could reflect the activities of disease- or injury-perturbed networks and collectively function as biomarkers for clinical disease diagnostics.

  10. Optimization of large-scale mouse brain connectome via joint evaluation of DTI and neuron tracing data.

    PubMed

    Chen, Hanbo; Liu, Tao; Zhao, Yu; Zhang, Tuo; Li, Yujie; Li, Meng; Zhang, Hongmiao; Kuang, Hui; Guo, Lei; Tsien, Joe Z; Liu, Tianming

    2015-07-15

    Tractography based on diffusion tensor imaging (DTI) data has been used as a tool by a large number of recent studies to investigate structural connectome. Despite its great success in offering unique 3D neuroanatomy information, DTI is an indirect observation with limited resolution and accuracy and its reliability is still unclear. Thus, it is essential to answer this fundamental question: how reliable is DTI tractography in constructing large-scale connectome? To answer this question, we employed neuron tracing data of 1772 experiments on the mouse brain released by the Allen Mouse Brain Connectivity Atlas (AMCA) as the ground-truth to assess the performance of DTI tractography in inferring white matter fiber pathways and inter-regional connections. For the first time in the neuroimaging field, the performance of whole brain DTI tractography in constructing a large-scale connectome has been evaluated by comparison with tracing data. Our results suggested that only with the optimized tractography parameters and the appropriate scale of brain parcellation scheme, can DTI produce relatively reliable fiber pathways and a large-scale connectome. Meanwhile, a considerable amount of errors were also identified in optimized DTI tractography results, which we believe could be potentially alleviated by efforts in developing better DTI tractography approaches. In this scenario, our framework could serve as a reliable and quantitative test bed to identify errors in tractography results which will facilitate the development of such novel tractography algorithms and the selection of optimal parameters. PMID:25953631

  11. Cell-type-specific neuroanatomy of cliques of autism-related genes in the mouse brain

    PubMed Central

    Grange, Pascal; Menashe, Idan; Hawrylycz, Michael

    2015-01-01

    Two cliques of genes identified computationally for their high co-expression in the mouse brain according to the Allen Brain Atlas, and for their enrichment in genes related to autism spectrum disorder (ASD), have recently been shown to be highly co-expressed in the cerebellar cortex, compared to what could be expected by chance. Moreover, the expression of these cliques of genes is not homogeneous across the cerebellar cortex, and it has been noted that their expression pattern seems to highlight the granular layer. However, this observation was only made by eye, and recent advances in computational neuroanatomy allow to rank cell types in the mouse brain (characterized by their transcriptome profiles) according to the similarity between their spatial density profiles and the spatial expression profiles of the cliques. We establish by Monte Carlo simulation that with probability at least 99%, the expression profiles of the two cliques are more similar to the density profile of granule cells than 99% of the expression of cliques containing the same number of genes (Purkinje cells also score above 99% in one of the cliques). Thresholding the expression profiles shows that the signal is more intense in the granular layer. Finally, we work out pairs of cell types whose combined expression profiles are more similar to the expression profiles of the cliques than any single cell type. These pairs predominantly consist of one cortical pyramidal cell and one cerebellar cell (which can be either a granule cell or a Purkinje cell). PMID:26074809

  12. MarsAtlas: A cortical parcellation atlas for functional mapping.

    PubMed

    Auzias, Guillaume; Coulon, Olivier; Brovelli, Andrea

    2016-04-01

    An open question in neuroimaging is how to develop anatomical brain atlases for the analysis of functional data. Here, we present a cortical parcellation model based on macroanatomical information and test its validity on visuomotor-related cortical functional networks. The parcellation model is based on a recently developed cortical parameterization method (Auzias et al., [2013]: IEEE Trans Med Imaging 32:873-887), called HIP-HOP. This method exploits a set of primary and secondary sulci to create an orthogonal coordinate system on the cortical surface. A natural parcellation scheme arises from the axes of the HIP-HOP model running along the fundus of selected sulci. The resulting parcellation scheme, called MarsAtlas, complies with dorsoventral/rostrocaudal direction fields and allows inter-subject matching. To test it for functional mapping, we analyzed a MEG dataset collected from human participants performing an arbitrary visuomotor mapping task. Single-trial high-gamma activity, HGA (60-120 Hz), was estimated using spectral analysis and beamforming techniques at cortical areas arising from a Talairach atlas (i.e., Brodmann areas) and MarsAtlas. Using both atlases, we confirmed that visuomotor associations involve an increase in HGA over the sensorimotor and fronto-parietal network, in addition to medial prefrontal areas. However, MarsAtlas provided: (1) crucial functional information along both the dorsolateral and rostrocaudal direction; (2) an increase in statistical significance. To conclude, our results suggest that the MarsAtlas is a valid anatomical atlas for functional mapping, and represents a potential anatomical framework for integration of functional data arising from multiple techniques such as MEG, intracranial EEG and fMRI. PMID:26813563

  13. Stereoselective rhodium-catalysed [2+2+2] cycloaddition of linear allene-ene/yne-allene substrates: reactivity and theoretical mechanistic studies.

    PubMed

    Haraburda, Ewelina; Torres, Óscar; Parella, Teodor; Solà, Miquel; Pla-Quintana, Anna

    2014-04-22

    Allene-ene-allene (2 and 5) and allene-yne-allene (3 and 7) N-tosyl and O-linked substrates were satisfactorily synthesised. The [2+2+2] cycloaddition reaction catalysed by the Wilkinson catalyst [RhCl(PPh3 )3 ] was evaluated. Substrates 2 and 5, which bear a double bond in the central position, gave a tricyclic structure in a reaction in which four contiguous stereogenic centres were formed as a single diastereomer. The reaction of substrates 3 and 7, which bear a triple bond in the central position, gave a tricyclic structure with a cyclohexenic ring core, again in a diastereoselective manner. All cycloadducts were formed by a regioselective reaction of the inner allene double bond and, therefore, feature an exocyclic diene motif. A Diels-Alder reaction on N-tosyl linked cycloadducts 8 and 10 allowed pentacyclic scaffolds to be diastereoselectively constructed. The reactivity of the allenes on [2+2+2] cycloaddition reactions was studied for the first time by density functional theory calculations. This mechanistic study rationalizes the order in which the unsaturations take part in the catalytic cycle, the reactivity of the two double bonds of the allene towards the [2+2+2] cycloaddition reaction, and the diastereoselectivity of the reaction.

  14. Atlas-based identification of cortical sulci

    NASA Astrophysics Data System (ADS)

    Nowinski, Wieslaw L.; Raphel, Jose K.; Nguyen, Bonnie T.

    1996-04-01

    The identification of cortical sulci is of great importance. In neurosurgical procedures any target in the cranium can be accessed by following the corridors of the sulci and fissures. The fusion of functional and anatomical data also requires the identification of sulci. Several approaches have been proposed for segmentation of the cortical surface and identification of sulci and fissures. Most of them are bottom-up. They work satisfactorily provided that the sulci are well discernible on MRI images, limiting their use to some major sulci and fissures, such as the central sulcus, interhemispheric fissure, or Sylvian fissure. We propose a sulcal model based approach, overcoming some of the above limitations. The sulcal model is derived from two brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach- Tournoux (TT), and Atlas of Cerebral Sulci by Ono-Kubik-Abernathey (OKA). The OKA atlas contains 403 patterns for 55 sulci along with their incidence rates of interruptions, side branches, and connections. An electronic version of the OKA atlas was constructed, quantitatively enhanced by placing the sulcal patterns in a stereotactic space. The original patterns from the OKA atlas were digitized, converted into geometric representation, placed in the Talairach stereotactic space, preregistered with the TT atlas, and integrated with a multi- atlas, multi-dimensional neuroimaging system developed by our group. The registration of any atlas with the clinical data automatically registers all atlases with this data. This way the sulcal patterns can be superimposed on data, indicating approximate locations of sulci on images. The approach proposed here provides a simple and real-time registration of the sulcal patterns with clinical data, and an interactive identification and labeling of sulci. This approach assists rather the medical professional, instead of providing a complete automated extraction of a few, primary sulci with certain accuracy, where a

  15. Automated pipeline for atlas-based annotation of gene expresssion patterns: application to postnatal day 7 mouse brain

    SciTech Connect

    Carson, James P.; Ju, Tao; Bello, Musodiq; Thaller, Christina; Warren, Joe; Kakadiaris, Ioannis; Chiu, Wah; Eichele, Gregor

    2010-02-01

    Abstract As bio-medical images and volumes are being collected at an increasing speed, there is a growing demand for efficient means to organize spatial information for comparative analysis. In many scenarios, such as determining gene expression patterns by in situ hybridization, the images are collected from multiple subjects over a common anatomical region, such as the brain. A fundamental challenge in comparing spatial data from different images is how to account for the shape variations among subjects, which makes direct image-to-image comparison meaningless. In this paper, we describe subdivision meshes as a geometric means to efficiently organize 2D images and 3D volumes collected from different subjects for comparison. The key advantages of a subdivision mesh for this purpose are its light-weight geometric structure and its explicit modeling of anatomical boundaries, which enable efficient and accurate registration. The multi-resolution structure of a subdivision mesh also allows development of fast comparison algorithms among registered images and volumes.

  16. Whole Brain Expression of Bipolar Disorder Associated Genes: Structural and Genetic Analyses

    PubMed Central

    McCarthy, Michael J.; Liang, Sherri; Spadoni, Andrea D.; Kelsoe, John R.; Simmons, Alan N.

    2014-01-01

    Studies of bipolar disorder (BD) suggest a genetic basis of the illness that alters brain function and morphology. In recent years, a number of genetic variants associated with BD have been identified. However, little is known about the associated genes, or brain circuits that rely upon their function. Using an anatomically comprehensive survey of the human transcriptome (The Allen Brain Atlas), we mapped the expression of 58 genes with suspected involvement in BD based upon their relationship to SNPs identified in genome wide association studies (GWAS). We then conducted a meta-analysis of structural MRI studies to identify brain regions that are abnormal in BD. Of 58 BD associated genes, 22 had anatomically distinct expression patterns that could be categorized into one of three clusters (C1–C3). Brain regions with the highest and lowest expression of these genes did not overlap strongly with anatomical sites identified as abnormal by structural MRI except in the parahippocampal gyrus, the inferior/superior temporal gyrus and the cerebellar vermis, regions where overlap was significant. Using the 22 genes in C1–C3 as reference points, additional genes with correlated expression patterns were identified and organized into sets based on similarity. Further analysis revealed that five of these gene sets were significantly associated with BD, suggesting that anatomical expression profile is correlated with genetic susceptibility to BD, particularly for genes in C2. Our data suggest that expression profiles of BD-associated genes do not explain the majority of structural abnormalities observed in BD, but may be useful in identifying new candidate genes. Our results highlight the complex neuroanatomical basis of BD, and reinforce illness models that emphasize impaired brain connectivity. PMID:24941232

  17. Hovering and forward flight energetics in Anna's and Allen's hummingbirds.

    PubMed

    Clark, Christopher James; Dudley, Robert

    2010-01-01

    Aerodynamic theory predicts that the mechanical costs of flight are lowest at intermediate flight speeds; metabolic costs of flight should trend similarly if muscle efficiency is constant. We measured metabolic rates for nine Anna's hummingbirds (Calypte anna) and two male Allen's hummingbirds (Selasphorus sasin) feeding during flight from a free-standing mask over a range of airspeeds. Ten of 11 birds exhibited higher metabolic costs during hovering than during flight at intermediate airspeeds, whereas one individual exhibited comparable costs at hovering and during forward flight up to speeds of approximately 7 m s(-1). Flight costs of all hummingbirds increased at higher airspeeds. Relative to Anna's hummingbirds, Allen's hummingbirds exhibited deeper minima in the power curve, possibly due to higher wing loadings and greater associated costs of induced drag. Although feeding at a mask in an airstream may reduce body drag and, thus, the contributions of parasite power to overall metabolic expenditure, these results suggest that hummingbird power curves are characterized by energetic minima at intermediate speeds relative to hovering costs. PMID:20455711

  18. Hovering and forward flight energetics in Anna's and Allen's hummingbirds.

    PubMed

    Clark, Christopher James; Dudley, Robert

    2010-01-01

    Aerodynamic theory predicts that the mechanical costs of flight are lowest at intermediate flight speeds; metabolic costs of flight should trend similarly if muscle efficiency is constant. We measured metabolic rates for nine Anna's hummingbirds (Calypte anna) and two male Allen's hummingbirds (Selasphorus sasin) feeding during flight from a free-standing mask over a range of airspeeds. Ten of 11 birds exhibited higher metabolic costs during hovering than during flight at intermediate airspeeds, whereas one individual exhibited comparable costs at hovering and during forward flight up to speeds of approximately 7 m s(-1). Flight costs of all hummingbirds increased at higher airspeeds. Relative to Anna's hummingbirds, Allen's hummingbirds exhibited deeper minima in the power curve, possibly due to higher wing loadings and greater associated costs of induced drag. Although feeding at a mask in an airstream may reduce body drag and, thus, the contributions of parasite power to overall metabolic expenditure, these results suggest that hummingbird power curves are characterized by energetic minima at intermediate speeds relative to hovering costs.

  19. Observations of Whistler-Mode Chorus with Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Kurth, William; Hospodarsky, George; Santolik, Ondrej; Kletzing, Craig; Bounds, Scott

    2014-10-01

    The Van Allen Probes mission provides an excellent opportunity to observe whistler-mode chorus and its role in the radiation belts. The plasma wave instrument on the two probes, called Waves, includes six identical waveform receivers covering the frequency range from 10 Hz to 12 kHz. The instrument measures three orthogonal magnetic field components and three orthogonal electric field components of waves. This complement supports wave-normal and Poynting flux analyses of chorus as well as other wave modes that interact with radiation belt particles. Extensive use of burst modes provides multicomponent waveforms enabling the study of individual chorus elements, including their substructure. The early-mission publications confirm the importance of chorus to the local acceleration of electrons in the outer radiation belts. The orbital precession of the twin Van Allen Probes through a complete range of local times now allows for a new survey of the distribution of chorus emissions. Hence, we now have the tools to study chorus from the nonlinear growth in chorus element substructures through synoptic studies of the near-equatorial occurrence of chorus out to a distance of approximately 5.8 Earth radii.

  20. Astronaut Andrew M. Allen, mission commander, sets up systems for a television downlink on the

    NASA Technical Reports Server (NTRS)

    1996-01-01

    STS-75 ONBOARD VIEW --- Astronaut Andrew M. Allen, mission commander, sets up systems for a television downlink on the flight deck of the Space Shuttle Columbia. Allen was joined by four other astronauts and an international payload specialist for more than 16 days of research aboard Columbia. The photograph was taken with a 70mm handheld camera.

  1. Q & A with Ed Tech Leaders: Interview with Michael W. Allen

    ERIC Educational Resources Information Center

    Shaughnessy, Michael F.

    2014-01-01

    Michael W. Allen, the Chairman and CEO of Allen Interactions, is an architect of interactive multimedia learning and is recognized for his many insights, inventions, and presentations. With over 50 years of experience in e-learning, both in academic and corporate settings, he is known for his role in creating Authorware and overseeing the work of…

  2. Highly Regioselective Radical Amination of Allenes: Direct Synthesis of Allenamides and Tetrasubstituted Alkenes.

    PubMed

    Zhang, Ge; Xiong, Tao; Wang, Zining; Xu, Guoxing; Wang, Xuedan; Zhang, Qian

    2015-10-19

    The first controllable, regioselective radical amination of allenes with N-fluoroarylsulfonimide is described to proceed under very mild reaction conditions. With this methodology, a general and straightforward route for the synthesis of both allenamides and fluorinated tetrasubstituted alkenes was realized from a wide range of terminal and internal allenes.

  3. Meeting the Challenge of Intermolecular Gold(I)-Catalyzed Cycloadditions of Alkynes and Allenes

    PubMed Central

    Muratore, Michael E; Homs, Anna; Obradors, Carla; Echavarren, Antonio M

    2014-01-01

    The development of gold(I)-catalyzed intermolecular carbo- and hetero-cycloadditions of alkynes and allenes has been more challenging than their intramolecular counterparts. Here we review, with a mechanistic perspective, the most fundamental intermolecular cycloadditions of alkynes and allenes with alkenes. PMID:25048645

  4. Ugi/Himbert Arene/Allene Diels-Alder Cycloaddition to Synthesize Strained Polycyclic Skeleton.

    PubMed

    Cheng, Guangsheng; He, Xiang; Tian, Lumin; Chen, Jiawen; Li, Chunju; Jia, Xueshun; Li, Jian

    2015-11-01

    The present work disclosed an efficient multicomponent reaction of isocyanide, allenic acid, aldehyde (ketone), and aniline. This protocol undergoes Ugi reaction followed by an intramolecular arene/allene Diels-Alder sequence, thus providing a rapid access to synthesize strained polycyclic skeletons.

  5. The Cerefy Neuroradiology Atlas: a Talairach-Tournoux atlas-based tool for analysis of neuroimages available over the internet.

    PubMed

    Nowinski, Wieslaw L; Belov, Dmitry

    2003-09-01

    The article introduces an atlas-assisted method and a tool called the Cerefy Neuroradiology Atlas (CNA), available over the Internet for neuroradiology and human brain mapping. The CNA contains an enhanced, extended, and fully segmented and labeled electronic version of the Talairach-Tournoux brain atlas, including parcelated gyri and Brodmann's areas. To our best knowledge, this is the first online, publicly available application with the Talairach-Tournoux atlas. The process of atlas-assisted neuroimage analysis is done in five steps: image data loading, Talairach landmark setting, atlas normalization, image data exploration and analysis, and result saving. Neuroimage analysis is supported by a near-real-time, atlas-to-data warping based on the Talairach transformation. The CNA runs on multiple platforms; is able to process simultaneously multiple anatomical and functional data sets; and provides functions for a rapid atlas-to-data registration, interactive structure labeling and annotating, and mensuration. It is also empowered with several unique features, including interactive atlas warping facilitating fine tuning of atlas-to-data fit, navigation on the triplanar formed by the image data and the atlas, multiple-images-in-one display with interactive atlas-anatomy-function blending, multiple label display, and saving of labeled and annotated image data. The CNA is useful for fast atlas-assisted analysis of neuroimage data sets. It increases accuracy and reduces time in localization analysis of activation regions; facilitates to communicate the information on the interpreted scans from the neuroradiologist to other clinicians and medical students; increases the neuroradiologist's confidence in terms of anatomy and spatial relationships; and serves as a user-friendly, public domain tool for neuroeducation. At present, more than 700 users from five continents have subscribed to the CNA.

  6. Atlas Mountains

    NASA Technical Reports Server (NTRS)

    2002-01-01

    These are the Anti-Atlas Mountains, part of the Atlas Mountain range in southern Morocco, Africa. The region contains some of the world's largest and most diverse mineral resources, most of which are still untouched. This image was acquired by Landsat 7's Enhanced Thematic Mapper plus (ETM+) sensor on June 22, 2001. This is a false-color composite image made using shortwave infrared, infrared, and red wavelengths. Image provided by the USGS EROS Data Center Satellite Systems Branch.

  7. Geomagnetic Storms and EMIC waves: Van Allen Probe observations

    NASA Astrophysics Data System (ADS)

    Wang, D.; Yuan, Z.; Yu, X.; Deng, X.; Zhou, M.; Huang, S.; Li, H.

    2015-12-01

    EMIC waves are believed to play an important role in the dynamics of ring current ions and radiation belt electrons, especially during geomagnetic storms. But, in which phase of the storm do the EMIC waves occur more is still under debate. Ground and some low altitude satellite observations demonstrate that EMIC waves are observed more frequently during the recovery phase, rather than during the main phase. Halford et al. 2010 looked at the occurrences of EMIC waves during 119 storms occurring throughout the CRRES mission. They found that 49 of the 119 (41%) storms observed EMIC waves and the majority, 56.25%, of storm time EMIC waves occurring during the main phase, while 35.57% in the recovery phase. One shortcoming of the CRRES mission is that the apogee of it did not covered the dawn to noon sector during its life time. Therefore, some dayside EMIC waves caused by the compression of magnetosphere may not be included in Halford et al 2010, as they mentioned. The apogee of Van Allen Probes covered all the MLT sectors from their launch to April 2014. Utilizing the data from magnetometer instrument on board the Van Allen Probe A, Wang et al. 2015 studied the occurrence rate of H-band and He-band EMIC waves in different MLT sectors, and Yu et al 2015 reported the O-band EMIC wave observations. In this work, we analysis the occurrence of EMIC waves during storms. According to the criteria of storm in Halford et al. 2010, we find 76 storms in our interested period, 8 September 2012 to 30 April 2014, when the apogee of Van Allen Probe A covered all the MLT sectors. To identify the onset of geomagnetic storm more accurately, we corrected the Sym-H index referred to Zhao and Zong (2011), which is helpful to demonstrate the activity of ring current. 50 of the 76 storms (66%) observed 124 EMIC wave events, in which 80 (64.5%) EMIC wave events are found in the recovery phase, more than the EMIC wave events in the main phase (35, 28.2%). The remaining 9 (7.3%) EMIC wave

  8. (Hetero)aromatics from dienynes, enediynes and enyne-allenes.

    PubMed

    Raviola, Carlotta; Protti, Stefano; Ravelli, Davide; Fagnoni, Maurizio

    2016-08-01

    The construction of aromatic rings has become a key objective for organic chemists. While several strategies have been developed for the functionalization of pre-formed aromatic rings, the direct construction of an aromatic core starting from polyunsaturated systems is yet a less explored field. The potential of such reactions in the formation of aromatics increased at a regular pace in the last few years. Nowadays, there are reliable and well-established procedures to prepare polyenic derivatives, such as dienynes, enediynes, enyne-allenes and hetero-analogues. This has stimulated their use in the development of innovative cycloaromatizations. Different examples have recently emerged, suggesting large potential of this strategy in the preparation of (hetero)aromatics. Accordingly, this review highlights the recent advancements in this field and describes the different conditions exploited to trigger the process, including thermal and photochemical activation, as well as the use of transition metal catalysis and the addition of electrophiles/nucleophiles or radical species.

  9. Ion spectral structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

    2015-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have reported single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). These ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. The HOPE mass spectrometer onboard the Van Allen Probes measures energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of nose-like structures, using 2-years measurements from the HOPE instrument. The results provide important details about the spatial distribution (dependence on geocentric distance), spectral features of the structures (differences among species), and geomagnetic conditions under which these structures occur.

  10. Van Allen Probe Charging During the St. Patrick's Day Event

    NASA Technical Reports Server (NTRS)

    Parker, L. Neergaard; Minow, J. I.

    2015-01-01

    The geomagnetic storms on and around March 17, 2015 marked the largest storms seen in the declining phase of the solar cycle to date. We use the Helium Oxygen Proton Electron (HOPE) mass spectrometer on board the Van Allen Probe - A and B satellites to study in detail the charging effects seen on these spacecraft during this time. Ion particle flux data provides information on the magnitude of the charging events using the ion line charging signature due to low energy ions accelerated by the spacecraft potential. Electron flux observations are used to correlate the charging environment with variations in spacecraft potential through the event. We also investigate the density and temperature of ions and electrons during the time of the charging event.

  11. The Allen telescope array: Commensal and efficient SETI

    NASA Astrophysics Data System (ADS)

    Deboer, David R.

    2006-12-01

    The Allen telescope array (ATA) currently under construction affords the possibility of a dedicated and highly efficient SETI program that may be done commensally with other radio astronomy programs. This symbiosis is important in order to maintain and sustain the long-term effort that may be required in order to achieve success as a positive or null result. The technology that is being exploited is the construction of many small elements that allow large fields-of-view at high sensitivity, the use of ultra-wideband front-ends, and the use of flexible digital “intermediate frequency (IF)” systems. The project is under construction in phases, with the first 32 antennas expected to be functional in the fall of 2004, the next 173 dishes operational early 2006, with plans for 350 antennas total within this decade.

  12. MRI atlas of the brain

    SciTech Connect

    Bradley, W.G. ); Bydder, G. )

    1990-01-01

    Since most radiologists will start from a basic of familiarity with pathophysiology of disease and a knowledge of cross-sectional imaging (at least in the transaxial plane), they are in a good position to recognize and diagnose many of the abnormalities we can currently see with CT. The appearance of these lesions on MRI is the basis for the majority of the images in this book. Chapters on Tumors, Infarcts and Ischemia, Demyelination and Infection. Hydrocephalus, and Pediatrics feature multiple images displaying the MR appearance of many common lesions with minimal associated text. Instead of focusing on pathophysiology, attention is directed to the variable appearance of these disease states using various MR imaging techniques. Although the MR contrast agent, Gadolinium-DTPA, has similar behavior (physiologically) to meglumine diatrizoate in CT, the MR techniques which result in optimal visualization of enhancing lesions are nonintuitive and are discussed. Similarly, the appearance of flowing blood and CSF and hemorrhage does not follow easily from a pre-existing CT base, therefore additional text has been devoted to these subjects.

  13. Revealing the Link Between Solar Activity and Satellite Anomalies: Career Recollections From Joe Allen

    NASA Astrophysics Data System (ADS)

    Schultz, Colin

    2012-08-01

    Beginning his career on the heels of the 1957-1958 International Geophysical Year and the dawn of the satellite era, Joe H. Allen entered the service of the U.S. Coast and Geodetic Survey in 1963. Earning a master's of science in engineering from the University of California at Berkeley while working for the Geodetic Survey, Allen advanced within a department that evolved into the National Geophysical Data Center, a branch of NOAA. Allen earned a Department of Commerce award in 1978 and in 1981 became the chief of the Solar and Terrestrial Physics Division of the National Geophysical Data Center, a position from which he retired in 1994.

  14. View-centralized multi-atlas classification for Alzheimer's disease diagnosis.

    PubMed

    Liu, Mingxia; Zhang, Daoqiang; Shen, Dinggang

    2015-05-01

    Multi-atlas based methods have been recently used for classification of Alzheimer's disease (AD) and its prodromal stage, that is, mild cognitive impairment (MCI). Compared with traditional single-atlas based methods, multiatlas based methods adopt multiple predefined atlases and thus are less biased by a certain atlas. However, most existing multiatlas based methods simply average or concatenate the features from multiple atlases, which may ignore the potentially important diagnosis information related to the anatomical differences among different atlases. In this paper, we propose a novel view (i.e., atlas) centralized multi-atlas classification method, which can better exploit useful information in multiple feature representations from different atlases. Specifically, all brain images are registered onto multiple atlases individually, to extract feature representations in each atlas space. Then, the proposed view-centralized multi-atlas feature selection method is used to select the most discriminative features from each atlas with extra guidance from other atlases. Next, we design a support vector machine (SVM) classifier using the selected features in each atlas space. Finally, we combine multiple SVM classifiers for multiple atlases through a classifier ensemble strategy for making a final decision. We have evaluated our method on 459 subjects [including 97 AD, 117 progressive MCI (p-MCI), 117 stable MCI (s-MCI), and 128 normal controls (NC)] from the Alzheimer's Disease Neuroimaging Initiative database, and achieved an accuracy of 92.51% for AD versus NC classification and an accuracy of 78.88% for p-MCI versus s-MCI classification. These results demonstrate that the proposed method can significantly outperform the previous multi-atlas based classification methods.

  15. Orion GNC Mitigation Efforts for Van Allen Radiation

    NASA Technical Reports Server (NTRS)

    King, Ellis T.; Jackson, Mark

    2013-01-01

    The Orion Crew Module (CM) is NASA's next generation manned space vehicle, scheduled to return humans to lunar orbit in the coming decade. The Orion avionics and GN&C architectures have progressed through a number of project phases and are nearing completion of a major milestone. The first unmanned test mission, dubbed "Exploration Flight Test One" (EFT-1) is scheduled to launch from NASA Kennedy Space Center late next year and provides the first integrated test of all the vehicle systems, avionics and software. The EFT-1 mission will be an unmanned test flight that includes a high speed re-entry from an elliptical orbit, which will be launched on an expendable launch vehicle (ELV). The ELV will place CM and the ELV upper stage into a low Earth orbit (LEO) for one revolution. After the first LEO, the ELV upper stage will re-ignite and place the combined upper stage/CM into an elliptical orbit whose perigee results in a high energy entry to test CM response in a relatively high velocity, high heating environment. While not producing entry velocities as high as those experienced in returning from a lunar orbit, the trajectory was chosen to provide higher stresses on the thermal protection and guided entry systems, as compared against a lower energy LEO entry. However the required entry geometry with constraints on inclination and landing site result in a trajectory that lingers for many hours in the Van Allen radiation belts. This exposes the vehicle and avionics to much higher levels of high energy proton radiation than a typical LEO or lunar trajectory would encounter. As a result, Van Allen radiation poses a significant risk to the Orion avionics system, and particularly the Flight Control Module (FCM) computers that house the GN&C flight software. The measures taken by the Orion GN&C, Flight Software and Avionics teams to mitigate the risks associated with the Van Allen radiation on EFT-1 are covered in the paper. Background on the Orion avionics subsystem is

  16. Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain.

    PubMed

    Krienen, Fenna M; Yeo, B T Thomas; Ge, Tian; Buckner, Randy L; Sherwood, Chet C

    2016-01-26

    The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute's human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections.

  17. Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain.

    PubMed

    Krienen, Fenna M; Yeo, B T Thomas; Ge, Tian; Buckner, Randy L; Sherwood, Chet C

    2016-01-26

    The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute's human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections. PMID:26739559

  18. Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain

    PubMed Central

    Krienen, Fenna M.; Yeo, B. T. Thomas; Ge, Tian; Buckner, Randy L.; Sherwood, Chet C.

    2016-01-01

    The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute’s human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections. PMID:26739559

  19. Branching Out: Rhodium-Catalyzed Allylation with Alkynes and Allenes.

    PubMed

    Koschker, Philipp; Breit, Bernhard

    2016-08-16

    We present a new and efficient strategy for the atom-economic transformation of both alkynes and allenes to allylic functionalized structures via a Rh-catalyzed isomerization/addition reaction which has been developed in our working group. Our methodology thus grants access to an important structural class valued in modern organic chemistry for both its versatility for further functionalization and the potential for asymmetric synthesis with the construction of a new stereogenic center. This new methodology, inspired by mechanistic investigations by Werner in the late 1980s and based on preliminary work by Yamamoto and Trost, offers an attractive alternative to other established methods for allylic functionalization such as allylic substitution or allylic oxidation. The main advantage of our methodology consists of the inherent atom economy in comparison to allylic oxidation or substitution, which both produce stoichiometric amounts of waste and, in case of the substitution reaction, require prefunctionalization of the starting material. Starting out with the discovery of a highly branched-selective coupling reaction of carboxylic acids with terminal alkynes using a Rh(I)/DPEphos complex as the catalyst system, over the past 5 years we were able to continuously expand upon this chemistry, introducing various (pro)nucleophiles for the selective C-O, C-S, C-N, and C-C functionalization of both alkynes and the double-bond isomeric allenes by choosing the appropriate rhodium/bidentate phosphine catalyst. Thus, valuable compounds such as branched allylic ethers, sulfones, amines, or γ,δ-unsaturated ketones were successfully synthesized in high yields and with a broad substrate scope. Beyond the branched selectivity inherent to rhodium, many of the presented methodologies display additional degrees of selectivity in regard to regio-, diastereo-, and enantioselective transformations, with one example even proceeding via a dynamic kinetic resolution. Many advances

  20. Iron‐catalyzed Cross‐Coupling of Propargyl Carboxylates and Grignard Reagents: Synthesis of Substituted Allenes

    PubMed Central

    Kessler, Simon N.

    2016-01-01

    Abstract Presented herein is a mild, facile, and efficient iron‐catalyzed synthesis of substituted allenes from propargyl carboxylates and Grignard reagents. Only 1–5 mol % of the inexpensive and environmentally benign [Fe(acac)3] at −20 °C was sufficient to afford a broad range of substituted allenes in excellent yields. The method tolerates a variety of functional groups. PMID:26890161

  1. Copper-catalyzed regio- and stereoselective intermolecular three-component oxyarylation of allenes.

    PubMed

    Itoh, Taisuke; Shimizu, Yohei; Kanai, Motomu

    2014-05-16

    A copper(II)-catalyzed intermolecular three-component oxyarylation of allenes using arylboronic acids as a carbon source and TEMPO as an oxygen source is described. The reaction proceeded under mild conditions with high regio- and stereoselectivity and functional group tolerance. A plausible reaction mechanism is proposed, involving carbocupration of allenes, homolysis of the intervening allylcopper(II), and a radical TEMPO trap. PMID:24766635

  2. Diastereoselective Synthesis of the Aminocyclitol Core of Jogyamycin via an Allene Aziridination Strategy

    PubMed Central

    Gerstner, Nels C.; Adams, Christopher S.; Grigg, R. David; Tretbar, Maik; Rigoli, Jared W.; Schomaker, Jennifer M.

    2016-01-01

    Oxidative allene amination provides rapid access to densely functionalized amine-containing stereotriads through highly reactive bicyclic methyleneaziridine intermediates. This strategy has been demonstrated as a viable approach for the construction of the densely functionalized aminocyclitol core of jogyamycin, a natural product with potent antiprotozoal activity. Importantly, the flexibility of oxidative allene amination will enable the syntheses of modified aminocyclitol analogues of the jogyamycin core. PMID:26741730

  3. Probable identity of Goltz syndrome and Van Allen-Myhre syndrome: evidence from phenotypic evolution.

    PubMed

    Hancock, Susan; Pryde, Peter; Fong, Christine; Brazy, Jane E; Stewart, Katharina; Favour, Amy; Pauli, Richard M

    2002-07-15

    We describe a girl who was diagnosed with split foot-split hand anomaly prenatally, in whom at birth the diagnosis of Van Allen-Myhre syndrome was made, and who at 8 months of age was recognized to have Goltz syndrome. Based on the evolution of clinical features in this infant, we suggest that our case, as well as that reported by Van Allen and Myhre, is an example of unusually severe Goltz syndrome.

  4. STS-46 Pilot Allen uses cycle ergometer on OV-104's middeck

    NASA Technical Reports Server (NTRS)

    1992-01-01

    STS-46 Pilot Andrew M. Allen exercises using the cycle ergometer on the middeck of Atlantis, Orbiter Vehicle (OV) 104. Allen, shirtless, is equipped with sensors for monitoring his biological systems during the exercise session. A communications kit assembly cable freefloats from his headset at his right and in front of the forward lockers. The open airlock hatch appears at his left and the sleep station behind him.

  5. Stereoselective nickel-catalyzed [2+2] cycloadditions of ene-allenes.

    PubMed

    Noucti, Njamkou N; Alexanian, Erik J

    2015-04-27

    A stereoselective nickel-catalyzed [2+2] cycloaddition of ene-allenes is reported. This transformation encompasses a broad range of ene-allene substrates, thus providing efficient access to fused cyclobutanes from easily accessed π-components. A simple and inexpensive first-row catalytic system comprised of [Ni(cod)2 ] and dppf was used in this process, thus constituting an attractive approach to synthetically challenging cyclobutane frameworks under mild reaction conditions.

  6. THE ALLEN TELESCOPE ARRAY SEARCH FOR ELECTROSTATIC DISCHARGES ON MARS

    SciTech Connect

    Anderson, Marin M.; Siemion, Andrew P. V.; Bower, Geoffrey C.; De Pater, Imke; Barott, William C.; Delory, Gregory T.; Werthimer, Dan

    2012-01-01

    The Allen Telescope Array was used to monitor Mars between 2010 March 9 and June 2, over a total of approximately 30 hr, for radio emission indicative of electrostatic discharge. The search was motivated by the report from Ruf et al. of the detection of non-thermal microwave radiation from Mars characterized by peaks in the power spectrum of the kurtosis, or kurtstrum, at 10 Hz, coinciding with a large dust storm event on 2006 June 8. For these observations, we developed a wideband signal processor at the Center for Astronomy Signal Processing and Electronics Research. This 1024 channel spectrometer calculates the accumulated power and power-squared, from which the spectral kurtosis is calculated post-observation. Variations in the kurtosis are indicative of non-Gaussianity in the signal, which can be used to detect variable cosmic signals as well as radio frequency interference (RFI). During the three-month period of observations, dust activity occurred on Mars in the form of small-scale dust storms; however, no signals indicating lightning discharge were detected. Frequent signals in the kurtstrum that contain spectral peaks with an approximate 10 Hz fundamental were seen at both 3.2 and 8.0 GHz, but were the result of narrowband RFI with harmonics spread over a broad frequency range.

  7. The Allen Telescope Array as Square Kilometer Array Pathfinder

    NASA Astrophysics Data System (ADS)

    Bower, Geoffrey C.

    2007-12-01

    The Allen Telescope Array (ATA) is a new radio interferometer that has begun scientific operations in 2007. Many of the technologies, techniques, and observing modes developed for the ATA are directly applicable to the Square Kilometer Array (SKA). The ATA is a pioneer of the LNSD, which refers to a large number (LN) of small diameter (SD) dishes to create the array. This concept underlies nearly all SKA designs. Other relevant technologies are the offset Gregorian ATA antenna, the ATA wideband log periodic feed, transport of broadband data over fiber optic cables, and flexible digital signal processing electronics. The small dishes of the ATA gives it extraordinary wide-field imaging and survey capability but also require new solutions for calibration and imaging. Real time imaging, rapid response to transients, and thinking telescope technology are also under development. Finally, the ATA is developing commensal observing modes, which enable multiple simultaneous science programs, such as SETI, transient surveys, and HI surveys. Opportunities exist for community members to perform scientific investigations as well as develop techniques and technology for the SKA through use of the ATA.

  8. The Benton-Van Allen faces: a lateralized tachistoscopic study.

    PubMed

    Püschel, J; Zaidel, E

    1994-03-01

    The Benton-Van Allen Facial Recognition Test (FRT) was adapted to a lateralized same-different task. The lateralized same targets were either physically identical to the central upright faces or had the same face identity but were transformed (3/4-views or shadowed faces). Faces were also modified to include or exclude external features. There was a left hemifield (right hemisphere) advantage only for the most difficult, shadowed faces. The absence of a left hemifield advantage for the matching of upright faces to identical or 3/4-view faces shows bilateral competence for face processing, both by physical and by face identity, and confirms previous observations that the FRT does not discriminate left from right hemisphere-damaged patients. Removal of external features affected performance in the right but not the left visual field, suggesting that the left hemisphere uses a less feature-dependent mechanism than the right hemisphere. This effect was only present in females, who were more lateralized than males.

  9. Wave acceleration of electrons in the Van Allen radiation belts.

    PubMed

    Horne, Richard B; Thorne, Richard M; Shprits, Yuri Y; Meredith, Nigel P; Glauert, Sarah A; Smith, Andy J; Kanekal, Shrikanth G; Baker, Daniel N; Engebretson, Mark J; Posch, Jennifer L; Spasojevic, Maria; Inan, Umran S; Pickett, Jolene S; Decreau, Pierrette M E

    2005-09-01

    The Van Allen radiation belts are two regions encircling the Earth in which energetic charged particles are trapped inside the Earth's magnetic field. Their properties vary according to solar activity and they represent a hazard to satellites and humans in space. An important challenge has been to explain how the charged particles within these belts are accelerated to very high energies of several million electron volts. Here we show, on the basis of the analysis of a rare event where the outer radiation belt was depleted and then re-formed closer to the Earth, that the long established theory of acceleration by radial diffusion is inadequate; the electrons are accelerated more effectively by electromagnetic waves at frequencies of a few kilohertz. Wave acceleration can increase the electron flux by more than three orders of magnitude over the observed timescale of one to two days, more than sufficient to explain the new radiation belt. Wave acceleration could also be important for Jupiter, Saturn and other astrophysical objects with magnetic fields.

  10. Geographical variation in bill size across bird species provides evidence for Allen's rule.

    PubMed

    Symonds, Matthew R E; Tattersall, Glenn J

    2010-08-01

    Allen's rule proposes that the appendages of endotherms are smaller, relative to body size, in colder climates, in order to reduce heat loss. Empirical support for Allen's rule is mainly derived from occasional reports of geographical clines in extremity size of individual species. Interspecific evidence is restricted to two studies of leg proportions in seabirds and shorebirds. We used phylogenetic comparative analyses of 214 bird species to examine whether bird bills, significant sites of heat exchange, conform to Allen's rule. The species comprised eight diverse taxonomic groups-toucans, African barbets, Australian parrots, estrildid finches, Canadian galliforms, penguins, gulls, and terns. Across all species, there were strongly significant relationships between bill length and both latitude and environmental temperature, with species in colder climates having significantly shorter bills. Patterns supporting Allen's rule in relation to latitudinal or altitudinal distribution held within all groups except the finches. Evidence for a direct association with temperature was found within four groups (parrots, galliforms, penguins, and gulls). Support for Allen's rule in leg elements was weaker, suggesting that bird bills may be more susceptible to thermoregulatory constraints generally. Our results provide the strongest comparative support yet published for Allen's rule and demonstrate that thermoregulation has been an important factor in shaping the evolution of bird bills. PMID:20545560

  11. Geographical variation in bill size across bird species provides evidence for Allen's rule.

    PubMed

    Symonds, Matthew R E; Tattersall, Glenn J

    2010-08-01

    Allen's rule proposes that the appendages of endotherms are smaller, relative to body size, in colder climates, in order to reduce heat loss. Empirical support for Allen's rule is mainly derived from occasional reports of geographical clines in extremity size of individual species. Interspecific evidence is restricted to two studies of leg proportions in seabirds and shorebirds. We used phylogenetic comparative analyses of 214 bird species to examine whether bird bills, significant sites of heat exchange, conform to Allen's rule. The species comprised eight diverse taxonomic groups-toucans, African barbets, Australian parrots, estrildid finches, Canadian galliforms, penguins, gulls, and terns. Across all species, there were strongly significant relationships between bill length and both latitude and environmental temperature, with species in colder climates having significantly shorter bills. Patterns supporting Allen's rule in relation to latitudinal or altitudinal distribution held within all groups except the finches. Evidence for a direct association with temperature was found within four groups (parrots, galliforms, penguins, and gulls). Support for Allen's rule in leg elements was weaker, suggesting that bird bills may be more susceptible to thermoregulatory constraints generally. Our results provide the strongest comparative support yet published for Allen's rule and demonstrate that thermoregulation has been an important factor in shaping the evolution of bird bills.

  12. Probabilistic maps of the white matter tracts with known associated functions on the neonatal brain atlas: Application to evaluate longitudinal developmental trajectories in term-born and preterm-born infants.

    PubMed

    Akazawa, Kentaro; Chang, Linda; Yamakawa, Robyn; Hayama, Sara; Buchthal, Steven; Alicata, Daniel; Andres, Tamara; Castillo, Deborrah; Oishi, Kumiko; Skranes, Jon; Ernst, Thomas; Oishi, Kenichi

    2016-03-01

    Diffusion tensor imaging (DTI) has been widely used to investigate the development of the neonatal and infant brain, and deviations related to various diseases or medical conditions like preterm birth. In this study, we created a probabilistic map of fiber pathways with known associated functions, on a published neonatal multimodal atlas. The pathways-of-interest include the superficial white matter (SWM) fibers just beneath the specific cytoarchitectonically defined cortical areas, which were difficult to evaluate with existing DTI analysis methods. The Jülich cytoarchitectonic atlas was applied to define cortical areas related to specific brain functions, and the Dynamic Programming (DP) method was applied to delineate the white matter pathways traversing through the SWM. Probabilistic maps were created for pathways related to motor, somatosensory, auditory, visual, and limbic functions, as well as major white matter tracts, such as the corpus callosum, the inferior fronto-occipital fasciculus, and the middle cerebellar peduncle, by delineating these structures in eleven healthy term-born neonates. In order to characterize maturation-related changes in diffusivity measures of these pathways, the probabilistic maps were then applied to DTIs of 49 healthy infants who were longitudinally scanned at three time-points, approximately five weeks apart. First, we investigated the normal developmental pattern based on 19 term-born infants. Next, we analyzed 30 preterm-born infants to identify developmental patterns related to preterm birth. Last, we investigated the difference in diffusion measures between these groups to evaluate the effects of preterm birth on the development of these functional pathways. Term-born and preterm-born infants both demonstrated a time-dependent decrease in diffusivity, indicating postnatal maturation in these pathways, with laterality seen in the corticospinal tract and the optic radiation. The comparison between term- and preterm

  13. Differences in the molecular structure of the blood-brain barrier in the cerebral cortex and white matter: an in silico, in vitro, and ex vivo study.

    PubMed

    Nyúl-Tóth, Ádám; Suciu, Maria; Molnár, Judit; Fazakas, Csilla; Haskó, János; Herman, Hildegard; Farkas, Attila E; Kaszaki, József; Hermenean, Anca; Wilhelm, Imola; Krizbai, István A

    2016-06-01

    The blood-brain barrier (BBB) is the main interface controlling molecular and cellular traffic between the central nervous system (CNS) and the periphery. It consists of cerebral endothelial cells (CECs) interconnected by continuous tight junctions, and closely associated pericytes and astrocytes. Different parts of the CNS have diverse functions and structures and may be subject of different pathologies, in which the BBB is actively involved. It is largely unknown, however, what are the cellular and molecular differences of the BBB in different regions of the brain. Using in silico, in vitro, and ex vivo techniques we compared the expression of BBB-associated genes and proteins (i.e., markers of CECs, brain pericytes, and astrocytes) in the cortical grey matter and white matter. In silico human database analysis (obtained from recalculated data of the Allen Brain Atlas), qPCR, Western blot, and immunofluorescence studies on porcine and mouse brain tissue indicated an increased expression of glial fibrillary acidic protein in astrocytes in the white matter compared with the grey matter. We have also found increased expression of genes of the junctional complex of CECs (occludin, claudin-5, and α-catenin) in the white matter compared with the cerebral cortex. Accordingly, occludin, claudin-5, and α-catenin proteins showed increased expression in CECs of the white matter compared with endothelial cells of the cortical grey matter. In parallel, barrier properties of white matter CECs were superior as well. These differences might be important in the pathogenesis of diseases differently affecting distinct regions of the brain.

  14. Chiral nonracemic alpha-alkylidene and alpha-silylidene cyclopentenones from chiral allenes using an intramolecular allenic Pauson-Khand-type cycloaddition.

    PubMed

    Brummond, Kay M; Kerekes, Angela D; Wan, Honghe

    2002-07-26

    We have successfully effected a transfer of chirality from a chiral nonracemic allene to an alpha-alkylidene and an alpha-silylidene cyclopentenone. The molybdenum-mediated examples possessing a silyl group on the terminus of the allene show good facial selectivities, but isomerization of the (E)-silylidene cyclopentenone to the (Z)-silylidene cyclopentenone occurs upon purification of these products. Alternatively, an alkyl group on the terminus of the allene undergoes cycloaddition with moderate selectivities but gives products that undergo an isomerization of the (Z)-alkylidene cyclopentenone to the (E)-alkylidene cyclopentenone when exposed to acidic conditions. Thus, erosion of the enantiomeric excesses is observed for one of the two products as a result of this isomerization. The allenic Pauson-Khand-type cycloaddition has also been effected by first isolation the (eta(6)-arene)molybdenum tricarbonyl complex, demonstrating for the first time that this is most likely the active complex in the molybdenum-mediated reactions. Attempts to increase the facial selectivity by increasing the size of the arene moiety resulted in a marginal increase in the selectivity at the expense of the yield. Based upon these results, we have concluded that altering the approach for the preparation of nonracemic alpha-alkylidene cyclopentenones is necessary in order to obtain synthetically useful levels of stereocontrol.

  15. Rhodium-catalyzed dynamic kinetic asymmetric transformations of racemic allenes by the [3+2] annulation of aryl ketimines.

    PubMed

    Tran, Duc N; Cramer, Nicolai

    2013-09-27

    Racemization required: Rhodium(I)-catalyzed C-H activation directed by unprotected ketimines initiates selective [3+2] cycloaddition with allenes, providing access to highly substituted indenylamines. The reaction proceeds through the dynamic kinetic asymmetric transformation of racemic allenes. The catalyst controls the enantio- and diastereoselectivity, the regioselectivities of the C-H activation and allene incorporation, as well as the E/Z ratio.

  16. Revealing latent value of clinically acquired CTs of traumatic brain injury through multi-atlas segmentation in a retrospective study of 1,003 with external cross-validation

    NASA Astrophysics Data System (ADS)

    Plassard, Andrew J.; Kelly, Patrick D.; Asman, Andrew J.; Kang, Hakmook; Patel, Mayur B.; Landman, Bennett A.

    2015-03-01

    Medical imaging plays a key role in guiding treatment of traumatic brain injury (TBI) and for diagnosing intracranial hemorrhage; most commonly rapid computed tomography (CT) imaging is performed. Outcomes for patients with TBI are variable and difficult to predict upon hospital admission. Quantitative outcome scales (e.g., the Marshall classification) have been proposed to grade TBI severity on CT, but such measures have had relatively low value in staging patients by prognosis. Herein, we examine a cohort of 1,003 subjects admitted for TBI and imaged clinically to identify potential prognostic metrics using a "big data" paradigm. For all patients, a brain scan was segmented with multi-atlas labeling, and intensity/volume/texture features were computed in a localized manner. In a 10-fold crossvalidation approach, the explanatory value of the image-derived features is assessed for length of hospital stay (days), discharge disposition (five point scale from death to return home), and the Rancho Los Amigos functional outcome score (Rancho Score). Image-derived features increased the predictive R2 to 0.38 (from 0.18) for length of stay, to 0.51 (from 0.4) for discharge disposition, and to 0.31 (from 0.16) for Rancho Score (over models consisting only of non-imaging admission metrics, but including positive/negative radiological CT findings). This study demonstrates that high volume retrospective analysis of clinical imaging data can reveal imaging signatures with prognostic value. These targets are suited for follow-up validation and represent targets for future feature selection efforts. Moreover, the increase in prognostic value would improve staging for intervention assessment and provide more reliable guidance for patients.

  17. A stereotaxic atlas for the telencephalon of the Siamese fighting fish (Betta splendens).

    PubMed

    Marino-Neto, J; Sabbatini, R M

    1988-01-01

    1. A stereotaxic technique for electrode positioning in the telencephalic nuclei of the Siamese Fighting fish (Betta splendens) is described. 2. The forebrain atlas was based on paraffin-embedded, in situ-sectioned, Nissl-stained material. Brain measurements were corrected for tissue shrinkage due to histological procedures. The atlas and methods have already been tested and have shown good accuracy and reproducibility.

  18. Space Weather data processing and Science Gateway for the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Romeo, G.; Barnes, R. J.; Weiss, M.; Fox, N. J.; Mauk, B.; Potter, M.; Kessel, R.

    2013-12-01

    A near real-time data processing pipeline for the Space Weather broadcast data from the Van Allen Probes is presented. The Van Allen Probes broadcasts a sub-set of the science data in real-time when not downlinking the principal science data. This broadcast is received by several ground stations and relayed to APL in near real time to be ingested into the space weather processing pipeline. This pipeline processes the available level zero space weather data into higher level science data products. These products are made available to the public via the Van Allen Probes Science Gateway website (http://athena.jhuapl.edu). The website acts as pivotal point though which all other instrument SOC's can be accessed. Several other data products (e.g KP/DST indices) and tools (e.g orbit calculator) are made also available to the general public.

  19. Conjugate observations of quasiperiodic emissions by the Cluster, Van Allen Probes, and THEMIS spacecraft

    NASA Astrophysics Data System (ADS)

    Němec, F.; Hospodarsky, G.; Pickett, J. S.; Santolík, O.; Kurth, W. S.; Kletzing, C.

    2016-08-01

    We present results of a detailed analysis of two electromagnetic wave events observed in the inner magnetosphere at frequencies of a few kilohertz, which exhibit a quasiperiodic (QP) time modulation of the wave intensity. The events were observed by the Cluster and Van Allen Probes spacecraft and in one event also by the THEMIS E spacecraft. The spacecraft were significantly separated in magnetic local time, demonstrating a huge azimuthal extent of the events. Geomagnetic conditions at the times of the observations were very quiet, and the events occurred inside the plasmasphere. The modulation period observed by the Van Allen Probes and THEMIS E spacecraft (duskside) was in both events about twice larger than the modulation period observed by the Cluster spacecraft (dawnside). Moreover, individual QP elements occur about 15 s earlier on THEMIS E than on Van Allen Probes, which might be related to a finite propagation speed of a modulating ULF wave.

  20. A C–H bond activation-based catalytic approach to tetrasubstituted chiral allenes

    PubMed Central

    Wu, Shangze; Huang, Xin; Wu, Wangteng; Li, Pengbin; Fu, Chunling; Ma, Shengming

    2015-01-01

    Enantioselective synthesis of fully substituted allenes has been a challenge due to the non-rigid nature of the axial chirality, which spreads over three carbon atoms. Here we show the commercially available simple Rh complex may catalyse the CMD (concerted metalation/deprotonation)-based reaction of the readily available arenes with sterically congested tertiary propargylic carbonates at ambient temperature affording fully substituted allenes. It is confirmed that the excellent designed regioselectivity for the C–C triple bond insertion is induced by the coordination of the carbonyl group in the directing carbonate group as well as the steric effect of the tertiary O-linked carbon atom. When an optically active carbonate was used, surprisingly high efficiency of chirality transfer was realized, affording fully substituted allenes in excellent enantiomeric excess (ee). PMID:26246391

  1. Spacecraft-level verification of the Van Allen Probes' RF communication system

    NASA Astrophysics Data System (ADS)

    Crowne, M. J.; Srinivasan, D.; Royster, D.; Weaver, G.; Matlin, D.; Mosavi, N.

    This paper presents the verification process, lessons learned, and selected test results of the radio frequency (RF) communication system of the Van Allen Probes, formerly known as the Radiation Belt Storm Probes (RBSP). The Van Allen Probes mission is investigating the doughnut-shaped regions of space known as the Van Allen radiation belts where the Sun interacts with charged particles trapped in Earth's magnetic field. Understanding this dynamic area that surrounds our planet is important to improving our ability to design spacecraft and missions for reliability and astronaut safety. The Van Allen Probes mission features two nearly identical spacecraft designed, built, and operated by the Johns Hopkins University Applied Physics Laboratory (JHU/APL) for the National Aeronautics and Space Administration (NASA). The RF communication system features the JHU/APL Frontier Radio. The Frontier Radio is a software-defined radio (SDR) designed for spaceborne communications, navigation, radio science, and sensor applications. This mission marks the first spaceflight usage of the Frontier Radio. RF ground support equipment (RF GSE) was developed using a ground station receiver similar to what will be used in flight and whose capabilities provided clarity into RF system performance that was previously not obtained until compatibility testing with the ground segments. The Van Allen Probes underwent EMC, acoustic, vibration, and thermal vacuum testing at the environmental test facilities at APL. During this time the RF communication system was rigorously tested to ensure optimal performance, including system-level testing down to threshold power levels. Compatibility tests were performed with the JHU/APL Satellite Communication Facility (SCF), the Universal Space Network (USN), and the Tracking and Data Relay Satellite System (TDRSS). Successful completion of this program as described in this paper validated the design of the system and demonstrated that it will be able to me

  2. A Century after Van Allen's Birth: Conclusion of Reconnaissance of Radiation Belts in the Solar System

    NASA Astrophysics Data System (ADS)

    Krimigis, S. M.

    2014-12-01

    On May 1, 1958 in the Great Hall of the US National Academy of Sciences, James A. Van Allen, having instrumented Explorer-1 and follow-on satellites with radiation detectors, announced the discovery of intense radiation at high altitudes above Earth. The press dubbed the doughnut-shaped structures "Van Allen Belts" (VAB). Soon thereafter, the search began for VAB at nearby planets. Mariner 2 flew by Venus in 1962 at a distance of 41,000 km, but no radiation was detected. The Mariner 4 mission to Mars did not observe planet-associated increase in radiation, but scaling arguments with Earth's magnetosphere yielded an upper limit to the ratio of magnetic moments of MM/ME < 0.001 (Van Allen et al, 1965). Similarly, the Mariner 5 flyby closer to Venus resulted in a ratio of magnetic moments < 0.001 (Van Allen et al, 1967), dealing a blow to the expectation that all planetary bodies must possess significant VAB. The flyby of Mercury in 1974 by Mariner 10 revealed a weak magnetic field, but the presence of durably trapped higher energy particles remained controversial until MESSENGER in 2011.The first flybys of Jupiter by Pioneers 10, 11 in 1973 and 1974, respectively, measured a plethora of energetic particles in Jupiter's magnetosphere and established the fact that their intensities were rotationally modulated. Later flybys of Jupiter and Saturn by the two Voyagers in 1979 and 1981 revealed that those magnetospheres possessed their own internal plasma source(s) and radiation belts. Subsequent discoveries of Van Allen belts at Uranus and Neptune by Voyager 2 demonstrated that VAB are the rule rather than the exception in planetary environments. We now know from the Voyagers and through Energetic Neutral Atom images from Cassini and IBEX that an immense energetic particle population surrounds the heliosphere itself. Thus, the reconnaissance of radiation belts of our solar system has been completed, some 56 years after the discovery of the Van Allen Belts at Earth.

  3. Prediction of tissue-specific effects of gene knockout on apoptosis in different anatomical structures of human brain

    PubMed Central

    2015-01-01

    Background An important issue in the target identification for the drug design is the tissue-specific effect of inhibition of target genes. The task of assessing the tissue-specific effect in suppressing gene activity is especially relevant in the studies of the brain, because a significant variability in gene expression levels among different areas of the brain was well documented. Results A method is proposed for constructing statistical models to predict the potential effect of the knockout of target genes on the expression of genes involved in the regulation of apoptosis in various brain regions. The model connects the expression of the objective group of genes with expression of the target gene by means of machine learning models trained on available expression data. Information about the interactions between target and objective genes is determined by reconstruction of target-centric gene network. STRING and ANDSystem databases are used for the reconstruction of gene networks. The developed models have been used to analyse gene knockout effects of more than 7,500 target genes on the expression of 1,900 objective genes associated with the Gene Ontology category "apoptotic process". The tissue-specific effect was calculated for 12 main anatomical structures of the human brain. Initial values of gene expression in these anatomical structures were taken from the Allen Brain Atlas database. The results of the predictions of the effect of suppressing the activity of target genes on apoptosis, calculated on average for all brain structures, were in good agreement with experimental data on siRNA-inhibition. Conclusions This theoretical paper presents an approach that can be used to assess tissue-specific gene knockout effect on gene expression of the studied biological process in various structures of the brain. Genes that, according to the predictions of the model, have the highest values of tissue-specific effects on the apoptosis network can be considered as

  4. Regiodivergent Intermolecular [3+2] Cycloadditions of Vinyl Aziridines and Allenes: Stereospecific Synthesis of Chiral Pyrrolidines.

    PubMed

    Lin, Tao-Yan; Zhu, Chao-Ze; Zhang, Peichao; Wang, Yidong; Wu, Hai-Hong; Feng, Jian-Jun; Zhang, Junliang

    2016-08-26

    The first rhodium-catalyzed intermolecular [3+2] cycloaddition reaction of vinyl aziridines and allenes for the synthesis of enantioenriched functionalized pyrrolidines was realized. [3+2] cycloaddition with the proximal C=C bond of N-allenamides gave 3-methylene-pyrrolidines in high regio- and diastereoselectivity, whereas, 2-methylene-pyrrolidines were obtained as the major products by the cycloadditions of vinyl aziridines with the distal C=C bond of allenes. Use of readily available starting materials, a broad substrate scope, high selectivity, mild reaction conditions, as well as versatile functionalization of the cycloadducts make this approach very practical and attractive. PMID:27485044

  5. Experiments in no-impact control of dingoes: comment on Allen et al. 2013.

    PubMed

    Johnson, Christopher N; Crowther, Mathew S; Dickman, Chris R; Letnic, Michael I; Newsome, Thomas M; Nimmo, Dale G; Ritchie, Euan G; Wallach, Arian D

    2014-01-01

    There has been much recent debate in Australia over whether lethal control of dingoes incurs environmental costs, particularly by allowing increase of populations of mesopredators such as red foxes and feral cats. Allen et al. (2013) claim to show in their recent study that suppression of dingo activity by poison baiting does not lead to mesopredator release, because mesopredators are also suppressed by poisoning. We show that this claim is not supported by the data and analysis reported in Allen et al.'s paper. PMID:24558973

  6. Diels–Alder Reactions of Allene with Benzene and Butadiene: Concerted, Stepwise, and Ambimodal Transition States

    PubMed Central

    2015-01-01

    Multiconfigurational complete active space methods (CASSCF and CASPT2) have been used to investigate the (4 + 2) cycloadditions of allene with butadiene and with benzene. Both concerted and stepwise radical pathways were examined to determine the mechanism of the Diels–Alder reactions with an allene dienophile. Reaction with butadiene occurs via a single ambimodal transition state that can lead to either the concerted or stepwise trajectories along the potential energy surface, while reaction with benzene involves two separate transition states and favors the concerted mechanism relative to the stepwise mechanism via a diradical intermediate. PMID:25216056

  7. Diels-Alder reactions of allene with benzene and butadiene: concerted, stepwise, and ambimodal transition states.

    PubMed

    Pham, Hung V; Houk, K N

    2014-10-01

    Multiconfigurational complete active space methods (CASSCF and CASPT2) have been used to investigate the (4 + 2) cycloadditions of allene with butadiene and with benzene. Both concerted and stepwise radical pathways were examined to determine the mechanism of the Diels-Alder reactions with an allene dienophile. Reaction with butadiene occurs via a single ambimodal transition state that can lead to either the concerted or stepwise trajectories along the potential energy surface, while reaction with benzene involves two separate transition states and favors the concerted mechanism relative to the stepwise mechanism via a diradical intermediate.

  8. Differentiating mechanistic possibilities for the thermal, intramolecular [2 + 2] cycloaddition of allene-ynes.

    PubMed

    Siebert, Matthew R; Osbourn, Joshua M; Brummond, Kay M; Tantillo, Dean J

    2010-09-01

    Intramolecular [2 + 2] cycloaddition reactions of allene-ynes offer a quick and efficient route to fused bicyclic ring structures. Insights into the mechanism and regiochemical preferences of this reaction are provided herein on the basis of the results of quantum chemical calculations (B3LYP/6-31+G(d,p)) and select experiments; both indicate that the reaction likely proceeds through a stepwise diradical pathway where one radical center is stabilized through allylic delocalization. The influences of the length of the tether connecting the alkyne and allene and substituent effects are also discussed.

  9. Copper-catalyzed regiodivergent silacarboxylation of allenes with carbon dioxide and a silylborane.

    PubMed

    Tani, Yosuke; Fujihara, Tetsuaki; Terao, Jun; Tsuji, Yasushi

    2014-12-24

    A regiodivergent silacarboxylation of allenes under a CO2 atmosphere with PhMe2Si-B(pin) as a silicon source in the presence of a copper catalyst at 70 °C has been developed. The regioselectivity of the reaction is successfully reversed by the proper choice of ligand; carboxylated vinylsilanes are obtained with rac-Me-DuPhos as the ligand, whereas the use of PCy3 affords carboxylated allylsilanes. Thus, two different carboxylated silanes can be selectively and regiodivergently synthesized from a single allene substrate. PMID:25469703

  10. Atlas of fetal sectional anatomy with ultrasound and magnetic resonance imaging

    SciTech Connect

    Isaacson, G.; Mintz, M.C.; Crelin, E.S.

    1986-01-01

    Here is an atlas of sectional anatomy for the fetus featuring correlated anatomy and imaging, transverse coronal and sagittal views, a guide to development of the brain, cardiac anatomy in standard plans of study and, over 280 illustrations.

  11. Intermolecular sequential [4 + 2]-cycloaddition-aromatization reaction of aryl-substituted allenes with DMAD affording phenanthrene and naphthalene derivatives.

    PubMed

    Jiang, Xuefeng; Kong, Wangqing; Chen, Jie; Ma, Shengming

    2008-10-01

    An efficient entry to phenanthrene and naphthalene derivatives through intermolecular sequential [4 + 2]-cycloaddition-aromatization reactions of aryl-substituted allenes with DMAD in the absence of any catalyst was discovered. In this reaction the aromatic ring and the adjacent carbon-carbon double bond of the allene unit acted as the 1,3-diene.

  12. Report to users of ATLAS

    SciTech Connect

    Ahmad, I.; Glagola, B.

    1995-05-01

    This report contains discussing in the following areas: Status of the Atlas accelerator; highlights of recent research at Atlas; concept for an advanced exotic beam facility based on Atlas; program advisory committee; Atlas executive committee; and Atlas and ANL physics division on the world wide web.

  13. ATLAS F MISSILE FIELDS IN THE UNITED STATES, ATLAS F ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    ATLAS F MISSILE FIELDS IN THE UNITED STATES, ATLAS F- TEXAS RING OF TWELVE - Dyess Air Force Base, Atlas F Missle Site S-8, Approximately 3 miles east of Winters, 500 feet southwest of Highway 177, Winters, Runnels County, TX

  14. Cobalt/rhodium heterobimetallic nanoparticle-catalyzed carbonylative [2+2+1] cycloaddition of allenes and bisallenes to Pauson-Khand-type reaction products.

    PubMed

    Park, Ji Hoon; Kim, Eunha; Kim, Hyeong-Mook; Choi, Soo Young; Chung, Young Keun

    2008-05-28

    The first catalytic intra- and intermolecular [2+2+1] cocyclization reactions of allenes and carbon monoxide have been developed. In the Co(2)Rh(2) heterobimetallic nanoparticle-catalyzed carbonylative [2+2+1] cycloaddition of allenes and carbon monoxide, the allenes formally serve both as an excellent alkene- and alkyne-like moiety within a Pauson-Khand-type process.

  15. Homoallylic amines by reductive inter- and intramolecular coupling of allenes and nitriles

    PubMed Central

    Manojlovic, Marija D

    2011-01-01

    Summary The one-pot hydrozirconation of allenes and nitriles followed by an in situ transmetalation of the allylzirconocene with dimethylzinc or zinc chloride provides functionalized homoallylic amines. An intramolecular version of this process leads to 3-aminotetrahydrofurans and 3-aminotetrahydropyrans. PMID:21804878

  16. Improving the Collection of Student Accounts at Allen County Community College.

    ERIC Educational Resources Information Center

    Geffert, Barbara

    During the past several years, Allen County Community College has experienced a growing number of uncollected student accounts. In an effort to encourage timely payment of student charges, lower the number of students receiving payment deferments, increase cash flow at the beginning of each semester, and reduce the number of bad debts being…

  17. The Native Speaker, the Student, and Woody Allen: Examining Traditional Roles in the Foreign Language Classroom.

    ERIC Educational Resources Information Center

    Finger, Anke

    This paper uses a language classroom role-playing scene from a Woody Allen movie to examine the language student who has traditionally been asked to emulate and copy the native speaker and to discuss roles that teachers ask students to play. It also presents the changing paradigm of the native speaker and his or her role inside and outside the…

  18. Rotationally resolved photoelectron spectroscopic study of the Jahn-Teller effect in allene

    NASA Astrophysics Data System (ADS)

    Schulenburg, A. M.; Merkt, F.

    2009-01-01

    The pulsed-field-ionization zero-kinetic-energy photoelectron spectra of allene (C3H4) and perdeuterated allene have been recorded from the first adiabatic ionization energy up to 2200 cm-1 of internal energy in the cations at a resolution sufficient to observe the full rotational structure. The intensity distributions in the spectra are dominated by vibrational progressions in the torsional mode, which were analyzed in the realm of a two-dimensional model of the E ⊗(b1⊕b2) Jahn-Teller effect in the allene cation [C. Woywod and W. Domcke, Chem. Phys. 162, 349 (1992)]. Whereas the rotational structure of the transitions to the lowest torsional levels (00 and 41) are regular and can be qualitatively analyzed in terms of a simple orbital ionization model, the rotational structure of the spectra of the 42 and 43 levels are strongly perturbed. The photoelectron spectrum of C3H4 also reveals several weak vibrational bands in the immediate vicinity of these levels that are indicative of (ro)vibronic perturbations. A slight broadening of the transitions to the 41 levels compared to that of the vibronic ground state and the increase of the number of sharp features in the rotational structure of the spectrum of the 42 level point at the importance of large-amplitude motions not considered in previous treatments of the Jahn-Teller effect in the allene cation.

  19. Astronauts Joseph Allen rides cherry picker over stowage area/work station

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Astronaut Joseph P. Allen rides a cherry picker over to a stowage area/work station to wrap up extravehicular activity (EVA) duties above Earth. The cherry picker is a union of the mobile foot restraint and the remote manipulator system (RMS), controlled from inside Discovery's cabin. The Westar VI/PAM-D satellite is pictured secured in Discovery's cargo bay.

  20. Regioselective Allene Hydrosilylation Catalyzed by NHC Complexes of Nickel and Palladium

    PubMed Central

    Miller, Zachary D.; Li, Wei; Belderrain, Tomás R.; Montgomery, John

    2013-01-01

    Regioselective methods for allene hydrosilylation have been developed, with regioselectivity being governed primarily by choice of metal. Alkenylsilanes are produced via nickel catalysis with larger N-heterocyclic carbene ligands, and allylsilanes are produced via palladium catalysis with smaller N-heterocyclic carbene ligands. These complementary methods allow either regioisomeric product to be obtained with exceptional regiocontrol. PMID:24079389

  1. Nathaniel Topliff Allen, Early Professional and 19th Century Risk Taker.

    ERIC Educational Resources Information Center

    Cadwallader, Lynn

    Nathaniel T. Allen's life (1823-1903) offers insights into 19th century professionalization of education in the United States. His independent political views set him apart as a strong-willed and dauntless supporter of equal education opportunity. Appointed by Horace Mann as principal of a model school connected with the first public normal school…

  2. An Interview with Dr. Roach van Allen (Leaders in Reading Research and Instruction).

    ERIC Educational Resources Information Center

    Searfoss, Lyndon; Jerrolds, Bob W.

    1989-01-01

    Presents an interview with Dr. Roach van Allen in which he describes how he became involved in education, who influenced him professionally, his proudest accomplishments (a theoretical model for a language experience program), what he sees as the current problems in reading education, and what he sees in the future. (RS)

  3. A Call to Action: JoBeth Allen, NCTE's 2012 Outstanding Educator in the Language Arts

    ERIC Educational Resources Information Center

    Tisdale, Carmen

    2012-01-01

    This article is a tribute to JoBeth Allen, recipient of the Elementary Section's 2012 award for Outstanding Educator in the English Language Arts. Each year, this award recognizes a distinguished educator who has made major contributions to the field of language arts in elementary education. This article was written by second-grade teacher and…

  4. All Together Now: Valerie Allen--U.S. Department of Energy

    ERIC Educational Resources Information Center

    Library Journal, 2005

    2005-01-01

    When Valerie Allen decided she did not want to be a Montessori teacher any longer, she began work on her MLIS. Immediately she learned concepts she could apply to her new job as information specialist for the Department of Energy's (DOE) Office of Scientific and Technical Information (OSTI) at Oak Ridge National Laboratory, TN. While the LIS…

  5. Precipitation of relativistic electrons of the Van Allen belts into the proton aurora

    SciTech Connect

    Jordanova, Vania K; Miyoshi, Y; Sakaguchi, K; Shiokawa, K; Evans, D S; Connors, M

    2008-01-01

    The Van Allen electron belts consist of two regions encircling the earth in which relativistic electrons are trapped in the earth's magnetic field. Populations of relativistic electrons in the Van Allen belts vary greatly with geomagnetic disturbance and they are a major source of damage to space vehicles. In order to know when and by how much these populations of relativistic electrons increase, it is important to elucidate not only the cause of acceleration of relativistic electrons but also the cause of their loss from the Van Allen belts. Here we show the first evidence that left-hand polarized electromagnetic ion cyclotron (EMIC) plasma waves can cause the loss of relativistic electrons into the atmosphere, on the basis of results of an excellent set of ground and satellite observations showing coincident precipitation of ions with energies of tens of keV and of relativistic electrons into an isolated proton aurora. The proton aurora was produced by precipitation of ions with energies of tens of keV due to EMIC waves near the plasma pause, which is a manifestation of wave-particle interactions. These observations clarify that ions with energies of tens of keV affect the evolution of relativistic electrons in the Van Allen belts via parasitic resonance with EMIC waves, an effect that was first theoretically predicted in the early 1970's.

  6. Rh(I)-Catalyzed Insertion of Allenes into C-C Bonds of Benzocyclobutenols.

    PubMed

    Zhao, Chunliang; Liu, Li-Chuan; Wang, Jing; Jiang, Chenran; Zhang, Qing-Wei; He, Wei

    2016-01-15

    Herein we report a Rh(I)-catalyzed two carbon insertion into C-C bonds of benzocyclobutenols by employing symmetrical and unsymmetrical allenes. This reaction provides rapid access to alkylidene tetralins bearing two adjacent stereogenic centers in good yields and diasteroselectivities.

  7. No Radio Flaring Detected from Cygnus X-3 at 3 GHz by Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Williams, P. K. G.; Bower, G. C.; Tomsick, J. A.; Bodaghee, A.; Corbet, R. H. D.

    2011-01-01

    Following the announcement of a 98 GHz flare from the microquasar Cygnus X-3 (ATel #3130), we observed it with the Allen Telescope Array (Welch et al., 2009 Proc. IEEE 97 1438 for 2.5 hours beginning at 2011 January 28.848 UT (MJD 55589.848), about 4.0 hours after the 98 GHz observations concluded.

  8. Complex polycyclic scaffolds by metathesis rearrangement of Himbert arene/allene cycloadducts.

    PubMed

    Lam, Jonathan K; Schmidt, Yvonne; Vanderwal, Christopher D

    2012-11-01

    The intramolecular arene/allene cycloaddition first described 30 years ago by Himbert and Henn permits rapid access to strained polycyclic compounds. Alkene metathesis processes cleanly rearrange appropriately substituted cycloadducts into complex, functional-group-rich polycyclic lactams of potential utility for natural product synthesis and medicinal chemistry.

  9. Highly selective cobalt-mediated [6 + 2] cycloaddition of cycloheptatriene and allenes.

    PubMed

    Clavier, Hervé; Le Jeune, Karel; de Riggi, Innocenzo; Tenaglia, Alphonse; Buono, Gérard

    2011-01-21

    [6 + 2] Cycloadditions between cycloheptatrienes with allenes have been investigated. Cobalt salts were found to promote this transformation efficiently. Moreover, this reaction was found to be highly selective since only one regioisomer was obtained with an excellent E/Z-selectivity.

  10. Studies on Lewis acid-mediated intramolecular cyclization reactions of allene-ene systems.

    PubMed

    Hiroi, K; Watanabe, T; Tsukui, A

    2000-03-01

    The Lewis acid-mediated reactions of allene-ene compounds, derived from 3-methylcitronellal or dimethyl malonate, were carried out using various Lewis acids such as ethylaluminum dichloride, diethylaluminum chloride, titanium chloride, zinc chloride etherate, or boron trifluoride etherate, affording unexpectedly intramolecular [2+2]cycloaddition products under some particular reaction conditions without any formation of intramolecular ene reaction products.

  11. Gold(I)-catalyzed enantioselective [4 + 2]-cycloaddition of allene-dienes.

    PubMed

    González, Ana Z; Toste, F Dean

    2010-01-01

    An enantioselective gold(I)-catalyzed intramolecular [4 + 2]-cycloaddition of allenes and dienes is reported. The reactions allow for the asymmetric synthesis of trans-hexahydroindenes and pyrrolidine products using C(3)-symmetric phosphitegold(I) and ortho-arylphosphoramiditegold(I) complexes as catalysts, respectively.

  12. Enantioselective [2 + 2 + 2] cycloaddition reaction of isocyanates and allenes catalyzed by nickel.

    PubMed

    Miura, Tomoya; Morimoto, Masao; Murakami, Masahiro

    2010-11-17

    The enantioselective intermolecular [2 + 2 + 2] cycloaddition reaction of two molecules of isocyanate and one molecule of allene is catalyzed by a nickel(0)/(S,S)-i-Pr-FOXAP complex, providing an efficient access to enantiomerically enriched dihydropyrimidine-2,4-diones.

  13. Gold-catalyzed stereocontrolled oxacyclization/[4+2]-cycloaddition cascade of ketone-allene substrates.

    PubMed

    Teng, Tse-Min; Liu, Rai-Shung

    2010-07-14

    We report the first success on the Au-catalyzed tandem oxacyclization/[4+2]-cycloaddition cascade using ketone-allene substrates to give highly substituted oxacyclics with excellent stereocontrol. In contrast to oxo-alkyne substrates, the resulting cycloadducts are isolable and efficiently produced from a reasonable scope of enol ethers.

  14. Gold(I)-catalyzed enantioselective [4 + 2]-cycloaddition of allene-dienes.

    PubMed

    González, Ana Z; Toste, F Dean

    2010-01-01

    An enantioselective gold(I)-catalyzed intramolecular [4 + 2]-cycloaddition of allenes and dienes is reported. The reactions allow for the asymmetric synthesis of trans-hexahydroindenes and pyrrolidine products using C(3)-symmetric phosphitegold(I) and ortho-arylphosphoramiditegold(I) complexes as catalysts, respectively. PMID:19961192

  15. New Results About the Earth’s Van Allen Radiation Belts

    NASA Astrophysics Data System (ADS)

    Baker, Daniel

    2015-01-01

    The first great scientific discovery of the Space Age was that the Earth is enshrouded in toroids, or 'belts', of very high-energy magnetically trapped charged particles. Early observations of the radiation environment clearly indicated that the Van Allen belts could be delineated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons in the energy range 100 keV < E< 1 MeV often populated both the inner and outer zones with a pronounced 'slot' region relatively devoid of energetic electrons existing between them. This two-belt structure for the Van Allen moderate-energy electron component was explained as being due to strong interactions of electrons with electromagnetic waves just inside the cold plasma (plasmapause) boundary. The energy distribution, spatial extent and particle species makeup of the Van Allen belts has been subsequently explored by several space missions. However, recent observations by the NASA dual-spacecraft Van Allen Probes mission have revealed wholly unexpected properties of the radiation belts, especially at highly relativistic (E > 2 MeV) and ultra-relativistic (E > 5 MeV) kinetic energies. In this presentation we show using high spatial and temporal resolution data from the Relativistic Electron-Proton Telescope (REPT) experiment on board the Van Allen Probes that multiple belts can exist concurrently and that an exceedingly sharp inner boundary exists for ultra-relativistic electrons. Using additionally available Van Allen Probes data, we demonstrate that these remarkable features of energetic electrons are not due to a physical boundary within Earth's intrinsic magnetic field. Neither is it likely that human-generated electromagnetic transmitter wave fields might produce such effects. Rather, we conclude from these unique measurements that slow natural inward radial diffusion combined with weak, but persistent, wave-particle pitch angle

  16. Intraoperative virtual brain counseling

    NASA Astrophysics Data System (ADS)

    Jiang, Zhaowei; Grosky, William I.; Zamorano, Lucia J.; Muzik, Otto; Diaz, Fernando

    1997-06-01

    Our objective is to offer online real-tim e intelligent guidance to the neurosurgeon. Different from traditional image-guidance technologies that offer intra-operative visualization of medical images or atlas images, virtual brain counseling goes one step further. It can distinguish related brain structures and provide information about them intra-operatively. Virtual brain counseling is the foundation for surgical planing optimization and on-line surgical reference. It can provide a warning system that alerts the neurosurgeon if the chosen trajectory will pass through eloquent brain areas. In order to fulfill this objective, tracking techniques are involved for intra- operativity. Most importantly, a 3D virtual brian environment, different from traditional 3D digitized atlases, is an object-oriented model of the brain that stores information about different brain structures together with their elated information. An object-oriented hierarchical hyper-voxel space (HHVS) is introduced to integrate anatomical and functional structures. Spatial queries based on position of interest, line segment of interest, and volume of interest are introduced in this paper. The virtual brain environment is integrated with existing surgical pre-planning and intra-operative tracking systems to provide information for planning optimization and on-line surgical guidance. The neurosurgeon is alerted automatically if the planned treatment affects any critical structures. Architectures such as HHVS and algorithms, such as spatial querying, normalizing, and warping are presented in the paper. A prototype has shown that the virtual brain is intuitive in its hierarchical 3D appearance. It also showed that HHVS, as the key structure for virtual brain counseling, efficiently integrates multi-scale brain structures based on their spatial relationships.This is a promising development for optimization of treatment plans and online surgical intelligent guidance.

  17. Computational analysis of LDDMM for brain mapping

    PubMed Central

    Ceritoglu, Can; Tang, Xiaoying; Chow, Margaret; Hadjiabadi, Darian; Shah, Damish; Brown, Timothy; Burhanullah, Muhammad H.; Trinh, Huong; Hsu, John T.; Ament, Katarina A.; Crocetti, Deana; Mori, Susumu; Mostofsky, Stewart H.; Yantis, Steven; Miller, Michael I.; Ratnanather, J. Tilak

    2013-01-01

    One goal of computational anatomy (CA) is to develop tools to accurately segment brain structures in healthy and diseased subjects. In this paper, we examine the performance and complexity of such segmentation in the framework of the large deformation diffeomorphic metric mapping (LDDMM) registration method with reference to atlases and parameters. First we report the application of a multi-atlas segmentation approach to define basal ganglia structures in healthy and diseased kids' brains. The segmentation accuracy of the multi-atlas approach is compared with the single atlas LDDMM implementation and two state-of-the-art segmentation algorithms—Freesurfer and FSL—by computing the overlap errors between automatic and manual segmentations of the six basal ganglia nuclei in healthy subjects as well as subjects with diseases including ADHD and Autism. The high accuracy of multi-atlas segmentation is obtained at the cost of increasing the computational complexity because of the calculations necessary between the atlases and a subject. Second, we examine the effect of parameters on total LDDMM computation time and segmentation accuracy for basal ganglia structures. Single atlas LDDMM method is used to automatically segment the structures in a population of 16 subjects using different sets of parameters. The results show that a cascade approach and using fewer time steps can reduce computational complexity as much as five times while maintaining reliable segmentations. PMID:23986653

  18. Adaptive local multi-atlas segmentation: application to the heart and the caudate nucleus.

    PubMed

    van Rikxoort, Eva M; Isgum, Ivana; Arzhaeva, Yulia; Staring, Marius; Klein, Stefan; Viergever, Max A; Pluim, Josien P W; van Ginneken, Bram

    2010-02-01

    Atlas-based segmentation is a powerful generic technique for automatic delineation of structures in volumetric images. Several studies have shown that multi-atlas segmentation methods outperform schemes that use only a single atlas, but running multiple registrations on volumetric data is time-consuming. Moreover, for many scans or regions within scans, a large number of atlases may not be required to achieve good segmentation performance and may even deteriorate the results. It would therefore be worthwhile to include the decision which and how many atlases to use for a particular target scan in the segmentation process. To this end, we propose two generally applicable multi-atlas segmentation methods, adaptive multi-atlas segmentation (AMAS) and adaptive local multi-atlas segmentation (ALMAS). AMAS automatically selects the most appropriate atlases for a target image and automatically stops registering atlases when no further improvement is expected. ALMAS takes this concept one step further by locally deciding how many and which atlases are needed to segment a target image. The methods employ a computationally cheap atlas selection strategy, an automatic stopping criterion, and a technique to locally inspect registration results and determine how much improvement can be expected from further registrations. AMAS and ALMAS were applied to segmentation of the heart in computed tomography scans of the chest and compared to a conventional multi-atlas method (MAS). The results show that ALMAS achieves the same performance as MAS at a much lower computational cost. When the available segmentation time is fixed, both AMAS and ALMAS perform significantly better than MAS. In addition, AMAS was applied to an online segmentation challenge for delineation of the caudate nucleus in brain MRI scans where it achieved the best score of all results submitted to date.

  19. Palladium-catalyzed synthesis of endocyclic allenes and their application in stereoselective [2 + 2]cycloaddition with ketenes.

    PubMed

    Ogasawara, Masamichi; Okada, Atsushi; Nakajima, Kiyohiko; Takahashi, Tamotsu

    2009-01-01

    Palladium-catalyzed reactions of various 2-bromo-3-exo-methylenecycloalkenes with a stabilized nucleophile were examined. When the carbocycles were nine-membered or larger, the corresponding endocyclic allenes were isolated in excellent yields. In a reaction of the eight-membered cyclic substrate, initial formation of a cycloocta-1,2-diene derivative was detected; however, it dimerized slowly. The seven-membered carbocycle was inert to the reaction. Using a chiral Pd-catalyst, an axially chiral endocyclic allene was obtained in 65% ee. The cyclic allenes were applied to [2 + 2]cycloaddition with ketenes, and the stereoselectivity was studied.

  20. Construction and application of human neonatal DTI atlases

    PubMed Central

    Deshpande, Rajiv; Chang, Linda; Oishi, Kenichi

    2015-01-01

    Atlas-based MRI analysis is one of many analytical methods and is used to investigate typical as well as abnormal neurodevelopment. It has been widely applied to the adult and pediatric populations. Successful applications of atlas-based analysis (ABA) in those cohorts have motivated the creation of a neonatal atlas and parcellation map (PM). The purpose of this review is to discuss the various neonatal diffusion tensor imaging (DTI) atlases that are available for use in ABA, examine how such atlases are constructed, review their applications, and discuss future directions in DTI. Neonatal DTI atlases are created from a template, which can be study-specific or standardized, and merged with the corresponding PM. Study-specific templates can retain higher image registration accuracy, but are usually not applicable across different studies. However, standardized templates can be used to make comparisons among various studies, but may not accurately reflect the anatomies of the study population. Methods such as volume-based template estimation are being developed to overcome these limitations. The applications for ABA, including atlas-based image quantification and atlas-based connectivity analysis, vary from quantifying neurodevelopmental progress to analyzing population differences in groups of neonates. ABA can also be applied to detect pathology related to prematurity at birth or exposure to toxic substances. Future directions for this method include research designed to increase the accuracy of the image parcellation. Methods such as multi-atlas label fusion and multi-modal analysis applied to neonatal DTI currently comprise an active field of research. Moreover, ABA can be used in high-throughput analysis to efficiently process medical images and to assess longitudinal brain changes. The overarching goal of neonatal ABA is application to the clinical setting, to assist with diagnoses, monitor disease progression and, ultimately, outcome prediction. PMID:26578899

  1. Visual Search of Neuropil-Enriched RNAs from Brain In Situ Hybridization Data through the Image Analysis Pipeline Hippo-ATESC

    PubMed Central

    Zongaro, Samantha; Bardoni, Barbara; Berto, Gaia; Bianchi, Federico; Molineris, Ivan; Giacobini, Mario; Cagnoni, Stefano; Di Cunto, Ferdinando

    2013-01-01

    Motivation RNA molecules specifically enriched in the neuropil of neuronal cells and in particular in dendritic spines are of great interest for neurobiology in virtue of their involvement in synaptic structure and plasticity. The systematic recognition of such molecules is therefore a very important task. High resolution images of RNA in situ hybridization experiments contained in the Allen Brain Atlas (ABA) represent a very rich resource to identify them and have been so far exploited for this task through human-expert analysis. However, software tools that may automatically address the same objective are not very well developed. Results In this study we describe an automatic method for exploring in situ hybridization data and discover neuropil-enriched RNAs in the mouse hippocampus. We called it Hippo-ATESC (Automatic Texture Extraction from the Hippocampal region using Soft Computing). Bioinformatic validation showed that the Hippo-ATESC is very efficient in the recognition of RNAs which are manually identified by expert curators as neuropil-enriched on the same image series. Moreover, we show that our method can also highlight genes revealed by microdissection-based methods but missed by human visual inspection. We experimentally validated our approach by identifying a non-coding transcript enriched in mouse synaptosomes. The code is freely available on the web at http://ibislab.ce.unipr.it/software/hippo/. PMID:24040258

  2. Multi-atlas learner fusion: An efficient segmentation approach for large-scale data.

    PubMed

    Asman, Andrew J; Huo, Yuankai; Plassard, Andrew J; Landman, Bennett A

    2015-12-01

    We propose multi-atlas learner fusion (MLF), a framework for rapidly and accurately replicating the highly accurate, yet computationally expensive, multi-atlas segmentation framework based on fusing local learners. In the largest whole-brain multi-atlas study yet reported, multi-atlas segmentations are estimated for a training set of 3464 MR brain images. Using these multi-atlas estimates we (1) estimate a low-dimensional representation for selecting locally appropriate example images, and (2) build AdaBoost learners that map a weak initial segmentation to the multi-atlas segmentation result. Thus, to segment a new target image we project the image into the low-dimensional space, construct a weak initial segmentation, and fuse the trained, locally selected, learners. The MLF framework cuts the runtime on a modern computer from 36 h down to 3-8 min - a 270× speedup - by completely bypassing the need for deformable atlas-target registrations. Additionally, we (1) describe a technique for optimizing the weak initial segmentation and the AdaBoost learning parameters, (2) quantify the ability to replicate the multi-atlas result with mean accuracies approaching the multi-atlas intra-subject reproducibility on a testing set of 380 images, (3) demonstrate significant increases in the reproducibility of intra-subject segmentations when compared to a state-of-the-art multi-atlas framework on a separate reproducibility dataset, (4) show that under the MLF framework the large-scale data model significantly improve the segmentation over the small-scale model under the MLF framework, and (5) indicate that the MLF framework has comparable performance as state-of-the-art multi-atlas segmentation algorithms without using non-local information.

  3. A Volume of Interest (VOI) Atlas for the Analysis of Neurophysiological Image Data

    NASA Astrophysics Data System (ADS)

    Marrett, Sean; Evans, Alan C.; Collins, D. L.; Peters, Terence M.

    1989-05-01

    Accurate and precise neuroanatomical descriptions are essential for the meaningful quantification of Positron Emission Tomographic (PET) images of the human brain. This task is difficult since the radio-tracer distribution imaged by PET does not neccessarily reflect structure. A two-dimensional brain atlas that features the use of a deformable Region-of-Interest (ROI) template has previously been shown to be an effective method for integrating anatomical (Magnetic Resonance Imaging - MRI) images and physiological (PET) data, with an observed reduction in the coefficient of variation amongst observers from 8.1% to 3.4% 1. This method has been adopted for routine MRI image correlation and PET image analysis at our centre. The atlas is most effective when used in studies in which PET and MRI images are acquired in planes parallel to those of the original brain atlas. To allow arbitrary image/atlas orientation, we have implemented a Volume of Interest (VOI) atlas that extends the ROI methodology to three dimensions. The major advantage is that, given adequate axial sampling, arbitrary orientations of PET and MRI scans can be matched to the VOI atlas with no loss in structural recovery. In addition, the VOI atlas can be employed in the quantification of metabolic parameters directly from volumetric PET studies rather than performing the analysis on a slice by slice basis.

  4. Shape-based multifeature brain parcellation

    NASA Astrophysics Data System (ADS)

    Nadeem, Saad; Kaufman, Arie

    2016-03-01

    We present a novel approach to parcellate - delineate the anatomical feature (folds, gyri, sulci) boundaries - the brain cortex. Our approach is based on extracting the 3D brain cortical surface mesh from magnetic resonance (MR) images, computing the shape measures (area, mean curvature, geodesic, and travel depths) for this mesh, and delineating the anatomical feature boundaries using these measures. We use angle-area preserving mapping of the cortical surface mesh to a simpler topology (disk or rectangle) to aid in the visualization and delineation of these boundaries. Contrary to commonly used generic 2D brain image atlas-based approaches, we use 3D surface mesh data extracted from a given brain MR imaging data and its specific shape measures for the parcellation. Our method does not require any non-linear registration of a given brain dataset to a generic atlas and hence, does away with the structure similarity assumption critical to the atlas-based approaches. We evaluate our approach using Mindboggle manually labeled brain datasets and achieve the following accuracies: 72.4% for gyri, 78.5% for major sulci, and 98.4% for folds. These results warrant further investigation of this approach as an alternative or as an initialization to the atlas-based approaches.

  5. Expression of concern: A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones.

    PubMed

    Kelly, Richard

    2015-12-21

    Expression of concern for 'A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones' by Adán B. González-Pérez et al., Org. Biomol. Chem., 2014, 12, 7694-7701.

  6. A Versatile Room-Temperature Route to Di- and Trisubstituted Allenes Using Flow-Generated Diazo Compounds.

    PubMed

    Poh, Jian-Siang; Tran, Duc N; Battilocchio, Claudio; Hawkins, Joel M; Ley, Steven V

    2015-06-26

    A copper-catalyzed coupling reaction between flow-generated unstabilized diazo compounds and terminal alkynes provides di- and trisubstituted allenes. This extremely mild and rapid transformation is highly tolerant of several functional groups.

  7. Novel synthesis of fused isoxazolidines via a palladium catalysed allene insertion-intramoleculer 1,3-dipolar cycloaddition cascade reaction.

    PubMed

    Aftab, Tajassas; Grigg, Ronald; Ladlow, Mark; Sridharan, Visuvanathar; Thornton-Pett, Mark

    2002-08-21

    A one pot, three component palladium catalysed allenation of aryl iodides, in combination with a nitrone cycloaddition, leads to formation of fused isoxazolidines, creating two rings, two stereocentres and one tetrasubstituted carbon centre.

  8. Nickel-iminophosphine-catalyzed [4+2] cycloaddition of enones with allenes: synthesis of highly substituted dihydropyrans.

    PubMed

    Sako, Saori; Kurahashi, Takuya; Matsubara, Seijiro

    2011-06-01

    Enones were found to react with allenes intermolecularly in the presence of a catalytic amount of a nickel-iminophosphine complex to provide dihydropyrans via oxidative cyclization of an enone and Ni(0).

  9. Rh(I)-catalyzed intramolecular [3 + 2] cycloaddition reactions of 1-ene-, 1-yne- and 1-allene-vinylcyclopropanes.

    PubMed

    Jiao, Lei; Lin, Mu; Yu, Zhi-Xiang

    2010-02-21

    New Rh(I)-catalyzed intramolecular [3 + 2] cycloaddition reactions of 1-ene-, 1-yne and 1-allene-vinylcyclopropanes have been developed, affording an efficient and versatile synthesis of cyclopentane- and cyclopentene-embedded bicyclic structures.

  10. Automated determination of electron density from electric field measurements on the Van Allen Probes spacecraft

    NASA Astrophysics Data System (ADS)

    Zhelavskaya, Irina; Kurth, William; Spasojevic, Maria; Shprits, Yuri

    2016-07-01

    We present the Neural-network-based Upper-hybrid Resonance Determination (NURD) algorithm for automatic inference of the electron number density from plasma wave measurements made onboard NASA's Van Allen Probes mission. A feedforward neural network is developed to determine the upper hybrid resonance frequency, f_{uhr}, from electric field measurements, which is then used to calculate the electron number density. In previous missions, the plasma resonance bands were manually identified, and there have been few attempts to do robust, routine automated detections. We describe the design and implementation of the algorithm and perform an initial analysis of the resulting electron number density distribution obtained by applying NURD to 2.5 years of data collected with the EMFISIS instrumentation suite of the Van Allen Probes mission. Densities obtained by NURD are compared to those obtained by another recently developed automated technique and also to an existing empirical plasmasphere and trough density model.

  11. Arthroscopic Medial Meniscus Posterior Root Fixation Using a Modified Mason-Allen Stitch

    PubMed Central

    Chung, Kyu Sung; Ha, Jeong Ku; Ra, Ho Jong; Kim, Jin Goo

    2016-01-01

    A complete radial tear of the meniscus posterior root, which can effectively cause a state of total meniscectomy via loss of hoop tension, requires that the torn root be repaired. Several methods have been used to repair medial meniscus posterior root tears, most of which are based on a simple stitch technique that is known to have stitch-holding strength. We applied a modified version of the Mason-Allen stitch technique, which is recognized as a method for rotator cuff repair surgery because its locking effect overcomes the potential weakness of simple stitches. This article introduces the medial meniscus posterior root tears repair procedure based on a modified Mason-Allen stitch technique in which 2 strands (i.e., 1 simple horizontal and 1 simple vertical stitch) are used. PMID:27073778

  12. Automated Determination of Electron Density from Electric Field Measurements on the Van Allen Probes Spacecraft

    NASA Astrophysics Data System (ADS)

    Zhelavskaya, Irina; Spasojevic, Maria; Shprits, Yuri; Kurth, William

    2016-04-01

    We present the Neural-network-based Upper-hybrid Resonance Determination (NURD) algorithm for automatic inference of the electron number density from plasma wave measurement made onboard NASA's Van Allen Probes mission. A feedforward neural network is developed to determine the upper hybrid resonance frequency, fuhr, from electric field measurements, which is then used to calculate the electron number density. In previous missions, the plasma resonance bands were manually identified, and there have been few attempts to do robust, routine automated detection. We describe the design and implementation of the algorithm and perform initial analysis of the resulting electron number density distribution obtained by applying NURD to 2.5 years of data collected with the EMFISIS instrumentation suite of the Van Allen Probes mission. Densities obtained by NURD are compared to those obtained by another recently developed automated technique and also to an existing empirical plasmasphere and trough density model.

  13. Automated determination of electron density from electric field measurements on the Van Allen Probes spacecraft

    NASA Astrophysics Data System (ADS)

    Zhelavskaya, I. S.; Spasojevic, M.; Shprits, Y. Y.; Kurth, W. S.

    2016-05-01

    We present the Neural-network-based Upper hybrid Resonance Determination (NURD) algorithm for automatic inference of the electron number density from plasma wave measurements made on board NASA's Van Allen Probes mission. A feedforward neural network is developed to determine the upper hybrid resonance frequency, fuhr, from electric field measurements, which is then used to calculate the electron number density. In previous missions, the plasma resonance bands were manually identified, and there have been few attempts to do robust, routine automated detections. We describe the design and implementation of the algorithm and perform an initial analysis of the resulting electron number density distribution obtained by applying NURD to 2.5 years of data collected with the Electric and Magnetic Field Instrument Suite and Integrated Science (EMFISIS) instrumentation suite of the Van Allen Probes mission. Densities obtained by NURD are compared to those obtained by another recently developed automated technique and also to an existing empirical plasmasphere and trough density model.

  14. Van Allen Probe Spacecraft Potential Fluctuations and Electromagnetic Waves: A Parameter Space Survey

    NASA Astrophysics Data System (ADS)

    Sturner, A. P.; Ergun, R.; Malaspina, D.

    2013-12-01

    The study of chorus waves, an important mechanism for the energization and loss of particles in the radiation belts and inner magnetosphere, has been significantly aided by observations of fluctuations in a spacecraft's potential, which have been shown to be correlated with plasma density structures. However, recent analysis of Van Allen Probe data suggests that the oscillatory electromagnetic fields of chorus waves may also induce spacecraft potential fluctuations via enhanced photoelectron escape, calling into question our understanding of chorus waves. We use a fully 3D particle tracing simulation to study the equilibrium potential of a model Van Allen Probe spacecraft under various plasma conditions, varying thermal temperature, electric and magnetic field strength, plasma density, etc., to better understand the parameter space under which enhanced photoelectron escape becomes important.

  15. Electron acceleration in the heart of the Van Allen radiation belts.

    PubMed

    Reeves, G D; Spence, H E; Henderson, M G; Morley, S K; Friedel, R H W; Funsten, H O; Baker, D N; Kanekal, S G; Blake, J B; Fennell, J F; Claudepierre, S G; Thorne, R M; Turner, D L; Kletzing, C A; Kurth, W S; Larsen, B A; Niehof, J T

    2013-08-30

    The Van Allen radiation belts contain ultrarelativistic electrons trapped in Earth's magnetic field. Since their discovery in 1958, a fundamental unanswered question has been how electrons can be accelerated to such high energies. Two classes of processes have been proposed: transport and acceleration of electrons from a source population located outside the radiation belts (radial acceleration) or acceleration of lower-energy electrons to relativistic energies in situ in the heart of the radiation belts (local acceleration). We report measurements from NASA's Van Allen Radiation Belt Storm Probes that clearly distinguish between the two types of acceleration. The observed radial profiles of phase space density are characteristic of local acceleration in the heart of the radiation belts and are inconsistent with a predominantly radial acceleration process.

  16. Portrait of an instrument-maker:Wenceslaus Hollar's engraving of Elias Allen.

    PubMed

    Higton, Hester

    2004-06-01

    Among the many engravings of landscapes, buildings, portraits and other illustrations produced by the seventeenth-century artist Wenceslaus Hollar, there are a small number of images of contemporary men of science. Of particular interest is the portrait of the instrument-maker Elias Allen, both because portraits of men of his social status were extremely uncommon at this time, and also because the cluttered mass of instruments shown in the image presents a picture wholly unlike other portraits of the period. The first part of this paper explores the position of portraiture as inherently linked to nobility, and seeks to present an explanation as to why the original oil painting of Allen (made by Hendrik van der Borcht and no longer extant) might have been made. The second part looks at the image itself, and discusses possible reasons for Hollar's production of the engraving some twenty years after the original.

  17. Gold-catalyzed intramolecular [3+2] cycloadditions of 1-aryl-1-allene-6-enes.

    PubMed

    Chaudhuri, Rupsha; Liao, Hsin-Yi; Liu, Rai-Shung

    2009-09-01

    Treatment of 1-aryl-1-allen-6-enes with [PPh(3)AuCl]/AgSbF(6) (5 mol %) in CH(2)Cl(2) at 25 degrees C led to intramolecular [3+2] cycloadditions, giving cis-fused dihydrobenzo[a]fluorene products efficiently and selectively. The reactions proceeded with initial formation of trans/cis mixtures of 2-alkyl-1-isopropyl-2-phenyl-1,2-dihydronaphthalene cations B, which were convertible into the desired cis-fused cycloadducts through the combined action of a gold catalyst and a Brønsted acid. Theoretic calculation supports the participation of the trans-B cation as reaction intermediate. Although HOTf showed similar activity towards several 1-aryl-1-allen-6-enes, it lacks generality for this cycloaddition reaction.

  18. Cycloaddition reactions of allenes with N-phenylmaleimide. A two-step, diradical-intermediate process

    SciTech Connect

    Pasto, D.J.; Heid, P.F.; Warren, S.E.

    1982-06-30

    The stereoselectivities, chemoselectivities, relative reactivities, and kinetic isotope effects have been determined in the cycloaddition reactions of substituted allenes with N-phenylmaleimide. The comparison of these results with those derived from the studies of the cycloaddition of 1,1-dichloro-2,2-difluoroethene and the radical-chain addition of benzenethiol to allenes strongly indicates that the cycloadditions with N-phenylmaleimide occur via a two-step, diradical-intermediate process. The stereochemical features controlling the formation of the stereoisomeric diradical intermediates and their ring closures are discussed. In addition to the cycloaddition processes, competitive ene reactions occur to produce intermediate dienes, which react further to produce 1:2 adducts or nonreactive alkyne-containing 1:1 adducts. These ene reactions also appear to proceed via diradical intermediates.

  19. National uranium resource evaluation: McAllen and Brownsville Quadrangles, Texas

    SciTech Connect

    Charepon, A J; Stauber, A J

    1982-06-01

    The McAllen and Brownsville Quadrangles, Texas, were evaluated to a depth of 1500 m to identify geologic environments and delineate areas favorable for uranium deposits. The environments were selected according to criteria established for the National Uranium Resource Evaluation program. Surface studies included investigations of uranium occurrences described in the literature, of locations of aerial radiometric anomalies, of surface exposures, and of locations of anomalous hydrogeochemical and stream-sediment reconnaissance data and collation of information on uranium exploration. Subsurface evaluation of selected geologic units was accomplished by using electric and gamma-ray well logs to construct maps and construct maps and cross sections. In the McAllen Quadrangle, an environment favorable for Texas roll-type sandstone uranium deposits is identified in 36 areas in the Goliad, Fleming-Oakville, Catahoula-Frio, and Whitsett Formations. All other units in both quadrangles are considered unfavorable.

  20. The commercial Atlas today

    NASA Astrophysics Data System (ADS)

    Patzer, Mike; White, Robert C.

    1990-07-01

    Spanning more than three decades, the General Dynamics Atlas launch vehicle program has contributed greatly to the productive exploitation of space. This paper briefly reviews Atlas history and achievements and then focuses on present Atlas launch vehicle configurations, capabilities, and propulsion systems. The four-vehicle Atlas family is described, inluding manufacturing, performance, and design differences. Vehicle launch options including the fairing and spacecraft adapter are discussed. A mission profile, flight environments, and a nominal sequence of events are described for a standard GTO mission. Details on vehicle enhancements are presented including the addition of solid rocket motors, booster and Centaur engine uprates, and avionics improvements.

  1. Reactions of two-coordinate phosphines with acetylenes: Synthesis of new allenic and acetylenic phosphines

    SciTech Connect

    Angelov, C.M.; Neilson, R.H. )

    1993-02-03

    The two-coordinate phosphines (Me[sub 3]Si)[sub 2]NP[double bond]ESiMe[sub 3] (1, E = N; 2, E = CH) reacted smoothly with 2-butyne via an ene process (instead of the expected cycloaddition reaction) to give the novel allenic phosphines H[sub 2]C[double bond]C[double bond]C(CH[sub 3])P[E(H)SiMe[sub 3

  2. Cooperative, highly enantioselective phosphinothiourea catalysis of imine-allene [3 + 2] cycloadditions.

    PubMed

    Fang, Yuan-Qing; Jacobsen, Eric N

    2008-04-30

    A new family of phosphinthiourea catalysts was developed for the highly enantioselective synthesis of 2-aryl-2,5-hydropyrroles via a [3 + 2] cycloaddition of an electron-deficient allene with aryl and heteroaryl diphenylphosphinoylimines. The presence of both H2O and Et3N as additives was found to be important for achieving optimal rates. Dual activation of both nucleophile and electrophile by the bifunctional catalyst is invoked to account for the observed high reactivity and enantioselectivity.

  3. The rα structure of allene: a study of solvent effects in NMR of oriented molecules

    NASA Astrophysics Data System (ADS)

    Diehl, P.; Baraldi, C.; Kellerhals, M.; Wasser, R.

    1987-11-01

    NMR spectra of partially oriented allene in 14 different liquid crystal solvents have been analyzed. The resulting direct couplings corrected for harmonic vibrations were used to determine the rα-structures. Considerable solvent effects were detected which disappeared, if the data were corrected also for the correlated molecule deformation. A solvent independent rα-structure which agreed well with IR results, and the interaction parameters of the CH and CC bonds of allene for all the solvents were determined.

  4. Gradual Diffusion and Punctuated Phase Space Density Enhancements of Highly Relativistic Electrons: Van Allen Probes Observations

    NASA Technical Reports Server (NTRS)

    Baker, D. N.; Jaynes, A. N.; Li, X.; Henderson, M. G.; Kanekal, S. G.; Reeves, G. D.; Spence, H. E.; Claudepierre, S. G.; Fennell, J. F.; Hudson, M. K.

    2014-01-01

    The dual-spacecraft Van Allen Probes mission has provided a new window into mega electron volt (MeV) particle dynamics in the Earth's radiation belts. Observations (up to E (is) approximately 10MeV) show clearly the behavior of the outer electron radiation belt at different timescales: months-long periods of gradual inward radial diffusive transport and weak loss being punctuated by dramatic flux changes driven by strong solar wind transient events. We present analysis of multi-MeV electron flux and phase space density (PSD) changes during March 2013 in the context of the first year of Van Allen Probes operation. This March period demonstrates the classic signatures both of inward radial diffusive energization and abrupt localized acceleration deep within the outer Van Allen zone (L (is) approximately 4.0 +/- 0.5). This reveals graphically that both 'competing' mechanisms of multi-MeV electron energization are at play in the radiation belts, often acting almost concurrently or at least in rapid succession.

  5. Van Allen Probes: Successful launch campaign and early operations exploring Earth's radiation belts

    NASA Astrophysics Data System (ADS)

    Kirby, K.; Stratton, J.

    The twin Van Allen Probe observatories developed at The Johns Hopkins University Applied Physics Laboratory for NASA's Heliophysics Division completed final observatory integration and environmental test activities and were successfully launched into orbit around the Earth on August 30, 2012. As the science operations phase begins, the mission is providing exciting new information about the impact of radiation belt activity on the earth. The on-board boom mounted magnetometers and other instruments are the most sensitive sensors of their type that have ever flown in the Van Allen radiation belts. The observatories are producing near-Earth space weather information that can be used to provide warnings of potential power grid interruptions or satellite damaging storms. The Van Allen Probes are operating in a challenging high radiation environment, and at the same time they are designed to make an insubstantial electric and magnetic field contribution to their surroundings. This paper will describe the challenges associated with observatory integration and test activities and observatory on-orbit checkout and commissioning. The lessons learned can be applied to other observatories and payloads that will be exposed to similar environments.

  6. Three acoustic forms of Allen's galagos (primates; Galagonidae) in the Central African region.

    PubMed

    Ambrose, Lesley

    2003-01-01

    This study identifies populations currently classified as Allen's galago (Galago alleni) at ten locations in Gabon, Cameroon and Bioko Island. Morphological diversity was evident both within and between populations. Attention to the loud calls revealed three distinct vocal profiles which are consistent within biogeographical regions. This work is based on the Recognition Concept of Species which refers to a Specific Mate Recognition System. Galagos rely less on visual signals than diurnal primates and recognise each other principally by means of auditory and olfactory signals. Galagos possess repertoires of loud calls relating to contact and alarm which are thought to be species-specific. Other studies of nocturnal prosimians (galagos, tarsiers) have demonstrated that the unique loud call repertoires are reliable indicators of species boundaries; whereas characters such as body size and pelage coloration are highly variable, even within populations. The vocal data in this study provide evidence of at least three acoustic forms of galago within the Allen's group which are predicted to represent three distinct species: the Allen's form on Bioko Island and south-west Cameroon, the Gabon form in southern Cameroon and northern Gabon and the Makandé form in Gabon south of the Ogooué river. Some populations may be vulnerable to extinction due to limited distributions and habitat destruction.

  7. Radition belt dynamics : Recent results from van Allen Probes and future observations from CeREs

    NASA Astrophysics Data System (ADS)

    Kanekal, Shrikanth; O'Brien, Paul; Baker, Daniel N.; Ogasawara, Keiichi; Fennell, Joseph; Christian, Eric; Claudepierre, Seth; Livi, Stefano; Desai, Mihir; Li, Xinlin; Jaynes, Allison; Turner, Drew; Jones, Ashley; Schiller, Quintin

    2016-07-01

    We describe recent observations of the Earth's radiation belts made by instruments on board the Van Allen Probes mission, particularly the Relativistic Electron Proton Telescope (REPT) and the Magnetic Electron Ion spectrometer (MagEIS). These observations have significantly advanced our understanding of terrestrial radiation belt dynamics. The Van Allen Probes mission comprises two identically instrumented spacecraft which were launched 31 August, 2012 into low-inclination lapping equatorial orbits. The orbit periods are about 9 hours, with perigees and apogees of of ~600 km and 5.8 RE respectively. We discuss the new scientific findings of the Van Allen Probes mission regarding the physics of energization and loss of relativistic electrons and their implications for future low-cost missions, especially CubeSats. We describe the CeREs (a Compact Radiation belt Explorer) CubeSat mission currently being built at the Goddard Space Flight Center, and carrying on board, an innovative instrument, the Miniaturized Electron Proton Telescope (MERiT). The MERiT is a compact low-mass low-power instrument measuring electrons from a few keV to tens of MeV in multiple differential channels. MERiT is optimized to measure electron microbursts with a high time resolution of a few milliseconds. We present and discuss possible future scientific contributions from CeREs.

  8. New Insight Into the Nightside Magnetosphere Ion Plasma Regimes With the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Jahn, J.; Goldstein, J.; Reeves, G. D.; Spence, H.; Skoug, R. M.; Funsten, H. O.

    2013-12-01

    The recent successful launch of the twin Van Allen spacecraft (formerly known as RBSP) provides a new and unprecedented window into the structure and dynamics of inner magnetospheric plasma content and dynamics. The equatorially orbiting Van Allen spacecraft are returning clean, high resolution, very low background ion composition and electron plasma data throughout the radiation belt and ring current region inside geosynchronous orbit. Since both Van Allen spacecraft are positioned in near-identical chase orbits, lapping each other continuously throughout the mission, we are able to study both spatial and temporal variability in the inner magnetosphere with unprecedented resolution on a range of time and length scales. In this paper we present initial results from plasma composition measurements in the nightside of Earth's magnetosphere, focusing on plasma fractional plasma composition of H+, He+, and O+ in the plasmasphere through lower ring current energies (< 50 keV). Early results indicate a remarkable spatial and temporal variability in plasma ion composition in the inner magnetosphere. We detect frequent occurrences of multiple peak energy distributions in this energy range occurring in ring current, plasmasphere and plasma sheet. We observe distinct differences between the three ion species in these spectra. Energy spectra with 5 peaks for a single species have been observed repeatedly. We discuss possible explanations for these observations, and possible ramifications for the evolution of the outer radiation belt.

  9. The Van Allen Probes first year of discovery and understanding (Invited)

    NASA Astrophysics Data System (ADS)

    Mauk, B.; Fox, N. J.; Sibeck, D. G.; Kanekal, S. G.; Kessel, R.

    2013-12-01

    The Van Allen Probes twin spacecraft were launched on 30 August 2012 and inserted into nearly identical, 1.1 x 5.8 RE elliptical, low inclination (10°), 9-hour period Earth orbits with one of the two spacecraft lapping the other about every 2.5 months. The discoveries and understandings achieved by the Van Allen Probes science investigations since the operational mission began on 1 November 2012 are all that we had hoped. The probes are discovering new and unanticipated behaviors of the radiation belts, for example coherently ordered multiple structures, and are revealing quantitatively how and why those behaviors occur. The probes are answering definitely outstanding important questions regarding Earth's inner magnetosphere, for example, the extent to which and the processes by which local acceleration contributes to creation of the belts. With its close 2-month coordination with the BARREL mission of opportunity array of Antarctic balloons, the Probes are contributing greatly to our understanding of the causes of radiation belt loss and the relationship between high and low altitude radiation belt phenomena. In this overview presentation we assess the discoveries and findings of the Van Allen Probes mission following its first year of operation, and provide a guide to the activities and achievements anticipated over the next year.

  10. New Insight into the Inner Magnetosphere Plasma Regimes with the van Allen Probes (RBSP)

    NASA Astrophysics Data System (ADS)

    Jahn, Joerg-Micha; Denton, Richard E.; Funsten, Herbert O.; Reeves, Geoff; Spence, Harlan E.

    2013-04-01

    The recent successful launch of the twin van Allen spacecraft (formerly known as RBSP) provides a new and unprecedented window into the structure and dynamics of inner magnetospheric plasma content and dynamics. The equatorially orbiting van Allen spacecraft are returning clean high resolution, very low background ion composition and electron plasma data throughout the radiation belt and ring current region inside geosynchronous orbit. Since both van Allen spacecraft are positioned in near-identical chase orbits, lapping each other continuously throughout the mission, we are able to study both spatial and temporal variability in the inner magnetosphere with unprecedented resolution on a range of time and length scales. In this paper we are presenting initial results from plasma composition measurements in the nightside of Earth's magnetosphere, focussing on plasma fractional plasma composition of H+, He+, and O+ in the plasmasphere through lower ring current energies (< 50 keV). Early results do not only indicate a remarkable spatial and temporal variability in plasma ion composition in the inner magnetosphere, they also show frequent occurrences of multiple peak energy distributions in this energy range. Multi-peaked energy distributions with several peaks occurring in ring current, plasmasphere and (less often) plasma sheet are frequently observed, with distinct differences between the three ion species. Energy spectra with 5-6 peaks for a single species have been observed repeatedly.

  11. Enhancements and Losses of Radiation Belt Particles: Van Allen Probes Observations

    NASA Astrophysics Data System (ADS)

    Baker, D. N.

    2015-12-01

    The dual-spacecraft Van Allen Probes mission has provided a new window into megaelectron Volt (MeV) particle dynamics in the Earth's radiation belts. Observations (up to E ~10 MeV) show clearly the behavior of the outer electron radiation belt at different time scales: months-long periods of gradual inward radial diffusive transport and weak loss being punctuated by dramatic flux changes driven by strong solar wind transient events. Analysis of multi-MeV electron flux and phase space density (PSD) changes during key intervals in March 2013 and March 2015 are presented in the context of the first three years of Van Allen Probes operation. These March periods demonstrate the classic signatures both of inward radial diffusive energization as well as abrupt localized acceleration deep within the outer Van Allen zone (L ~4.0±0.5). Such results reveal graphically that both "competing" mechanisms of multi-MeV electron energization are at play in the radiation belts, often acting almost concurrently or at least in very rapid succession. They also show in remarkable ways how the coldest plasmas in the magnetosphere intimately control the most highly energetic particles.

  12. Observation of plasma depletions in outer radiation belt by Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Lee, J.; Kim, K.; Lee, E.; Kim, Y.; Park, Y.; Parks, G. K.; Sibeck, D. G.

    2013-12-01

    Van Allen Probes (RBSP) observed plasma fine structures in the outer radiation belt during storm time on 14 November 2012. Five plasma depletion regions are clearly identified by VAP_A and VAP_B from 02:00UT to 04:45UT by particle instrument suite that can measure electrons and ions in a wide energy range, from 20 eV to 10 MeV. The plasma flux density dramatically decreases about 2 - 3 orders of magnitude in the depletion regions regardless of energy and particle species. Our analysis shows the plasma cavities are formed at the boundary of trapped and injected particle current. The total plasma pressures inside the depletion regions are much smaller than outside, implying unstable structures. It seems that this structures appear unusually only for storm main phase. During strong storm event, geomagnetic field is stretched and low plasma density region (lobe) moves to low latitude, this event could be analyzed by lobe region crossing of spacecraft. However, to explain temporal sequences of this event, we should assume large fluctuation of lobe boundary. Another possible analysis is plasma bubble generated in the tail region. The bubble model proposed to explain plasma transportation form tail to near Earth region in 1980s. While the bubble model reasonably explain the spatial and temporal structures observed by Van Allen probes, we cannot completely rule out the lobe region crossing model. In this presentation, we shall discuss about the characteristics of the plasma density cavities first observed by Van Allen Probes.

  13. A neural network approach for identifying particle pitch angle distributions in Van Allen Probes data

    NASA Astrophysics Data System (ADS)

    Souza, V. M.; Vieira, L. E. A.; Medeiros, C.; Da Silva, L. A.; Alves, L. R.; Koga, D.; Sibeck, D. G.; Walsh, B. M.; Kanekal, S. G.; Jauer, P. R.; Rockenbach, M.; Dal Lago, A.; Silveira, M. V. D.; Marchezi, J. P.; Mendes, O.; Gonzalez, W. D.; Baker, D. N.

    2016-04-01

    Analysis of particle pitch angle distributions (PADs) has been used as a means to comprehend a multitude of different physical mechanisms that lead to flux variations in the Van Allen belts and also to particle precipitation into the upper atmosphere. In this work we developed a neural network-based data clustering methodology that automatically identifies distinct PAD types in an unsupervised way using particle flux data. One can promptly identify and locate three well-known PAD types in both time and radial distance, namely, 90° peaked, butterfly, and flattop distributions. In order to illustrate the applicability of our methodology, we used relativistic electron flux data from the whole month of November 2014, acquired from the Relativistic Electron-Proton Telescope instrument on board the Van Allen Probes, but it is emphasized that our approach can also be used with multiplatform spacecraft data. Our PAD classification results are in reasonably good agreement with those obtained by standard statistical fitting algorithms. The proposed methodology has a potential use for Van Allen belt's monitoring.

  14. Functional analysis of allene oxide cyclase, MpAOC, in the liverwort Marchantia polymorpha.

    PubMed

    Yamamoto, Yusuke; Ohshika, Jun; Takahashi, Tomohiro; Ishizaki, Kimitsune; Kohchi, Takayuki; Matusuura, Hideyuki; Takahashi, Kosaku

    2015-08-01

    12-Oxo-phytodienoic acid (OPDA) is an intermediate in jasmonic acid (JA) biosynthesis. OPDA exerts JA-dependent and JA-independent biological effects; therefore, it is considered a signaling molecule in flowering plants. OPDA is induced by bacterial infection and wounding and inhibits growth in the moss Physcomitrella patens. The functions of OPDA and allene oxide cyclase (AOC) in the liverwort Marchantia polymorpha were explored, which represents the most basal lineage of extant land plants. The analysis of OPDA showed that it is present in M. polymorpha and is increased by wounding. OPDA has been suggested to be involved in the response to environmental stresses. Moreover, OPDA showed growth inhibitory activity in M. polymorpha. Nonetheless JA in M. polymorpha was not found in this study. AOC synthesizes OPDA from an unstable allene oxide. A database search of the M. polymorpha genome identified only a putative gene encoding allene oxide cyclase (MpAOC). Recombinant MpAOC showed AOC activity similar to that in flowering plants. MpAOC was localized to chloroplasts, as in flowering plants. Expression of MpAOC was induced by wounding and OPDA treatment, and positive feedback regulation of OPDA was demonstrated in M. polymorpha. Overexpression of MpAOC increased the endogenous OPDA level and suppressed growth in M. polymorpha. These results indicate the role of OPDA as a signaling molecule regulating growth and the response to wounding in the liverwort M. polymorpha. PMID:25892411

  15. An Impenetrable Barrier to Ultra-Relativistic Electrons in the Van Allen Radiation Belt

    NASA Astrophysics Data System (ADS)

    Baker, Daniel

    2015-04-01

    Early observations indicated that the Earth's Van Allen belts could be delineated into an inner zone dominated by high energy protons and an outer zone dominated by high energy electrons. Subsequent studies showed that moderate-energy electrons (E≲1 MeV) often populate both zones with a deep "slot" region between them. This two-belt structure was explained as being due to strong electron interactions with plasmaspheric hiss just inside the plasmapause boundary with the inner edge of the outer zone corresponding to the minimum plasmapause location. Recent Van Allen Probes observations have revealed unexpected radiation belt morphology, especially at ultra-relativistic (E > 5 MeV) kinetic energies. Here we discuss an exceedingly sharp inner boundary exists for ultra-relativistic electrons. Concurrent data reveal that this barrier for inward electron radial transport is not due to a physical boundary within Earth's intrinsic magnetic field nor is it likely that scattering by human-generated electromagnetic transmitter wave fields would inhibit inward radial diffusion. Rather, we suggest that exceptionally slow natural inward radial diffusion combined with weak, but persistent, wave-particle pitch angle scattering deep inside the Earth's plasmasphere can conspire to create an almost impenetrable barrier through which the most energetic Van Allen belt electrons cannot migrate.

  16. Two-stage atlas subset selection in multi-atlas based image segmentation

    SciTech Connect

    Zhao, Tingting Ruan, Dan

    2015-06-15

    Purpose: Fast growing access to large databases and cloud stored data presents a unique opportunity for multi-atlas based image segmentation and also presents challenges in heterogeneous atlas quality and computation burden. This work aims to develop a novel two-stage method tailored to the special needs in the face of large atlas collection with varied quality, so that high-accuracy segmentation can be achieved with low computational cost. Methods: An atlas subset selection scheme is proposed to substitute a significant portion of the computationally expensive full-fledged registration in the conventional scheme with a low-cost alternative. More specifically, the authors introduce a two-stage atlas subset selection method. In the first stage, an augmented subset is obtained based on a low-cost registration configuration and a preliminary relevance metric; in the second stage, the subset is further narrowed down to a fusion set of desired size, based on full-fledged registration and a refined relevance metric. An inference model is developed to characterize the relationship between the preliminary and refined relevance metrics, and a proper augmented subset size is derived to ensure that the desired atlases survive the preliminary selection with high probability. Results: The performance of the proposed scheme has been assessed with cross validation based on two clinical datasets consisting of manually segmented prostate and brain magnetic resonance images, respectively. The proposed scheme demonstrates comparable end-to-end segmentation performance as the conventional single-stage selection method, but with significant computation reduction. Compared with the alternative computation reduction method, their scheme improves the mean and medium Dice similarity coefficient value from (0.74, 0.78) to (0.83, 0.85) and from (0.82, 0.84) to (0.95, 0.95) for prostate and corpus callosum segmentation, respectively, with statistical significance. Conclusions: The authors

  17. Generation and evaluation of an ultra-high-field atlas with applications in DBS planning

    NASA Astrophysics Data System (ADS)

    Wang, Brian T.; Poirier, Stefan; Guo, Ting; Parrent, Andrew G.; Peters, Terry M.; Khan, Ali R.

    2016-03-01

    Purpose Deep brain stimulation (DBS) is a common treatment for Parkinson's disease (PD) and involves the use of brain atlases or intrinsic landmarks to estimate the location of target deep brain structures, such as the subthalamic nucleus (STN) and the globus pallidus pars interna (GPi). However, these structures can be difficult to localize with conventional clinical magnetic resonance imaging (MRI), and thus targeting can be prone to error. Ultra-high-field imaging at 7T has the ability to clearly resolve these structures and thus atlases built with these data have the potential to improve targeting accuracy. Methods T1 and T2-weighted images of 12 healthy control subjects were acquired using a 7T MR scanner. These images were then used with groupwise registration to generate an unbiased average template with T1w and T2w contrast. Deep brain structures were manually labelled in each subject by two raters and rater reliability was assessed. We compared the use of this unbiased atlas with two other methods of atlas-based segmentation (single-template and multi-template) for subthalamic nucleus (STN) segmentation on 7T MRI data. We also applied this atlas to clinical DBS data acquired at 1.5T to evaluate its efficacy for DBS target localization as compared to using a standard atlas. Results The unbiased templates provide superb detail of subcortical structures. Through one-way ANOVA tests, the unbiased template is significantly (p <0.05) more accurate than a single-template in atlas-based segmentation and DBS target localization tasks. Conclusion The generated unbiased averaged templates provide better visualization of deep brain nuclei and an increase in accuracy over single-template and lower field strength atlases.

  18. [A study on Horace N. Allen's medicine and recognition of Korean body].

    PubMed

    Lee, Young Ah

    2011-12-31

    Je Jung Won was the first modern-style Government hospital built by the Korean King Ko-Jong in April 1885, and it was the medical missionary Horace Newton Allen(1858~1932) who made one of the greatest contributions to the establishment of the hospital. Allen was an American missionary. He graduated from Ohio Wesleyan University with a degree in theology in 1881, and completed one-yearcourse at Miami Medical College. In Korea and America he worked as a physician, a missionary, an American diplomatic minister to Korea and a Korean minister's secretary to America. While acting as a mediator between Korea and America, he knew and recorded the domestic and foreign situation of Korea during Gaehwagi(the civilized and enlightened age). Thus to study him is to understand Korea's Gaehwagi as well as to research American medical missionaries. During his stay in Korea(1884~1905), Allen steadily wrote diaries and letters about Korean politics, diplomacy, society, culture, and medicine. Thus his public/private record through diaries and letters(the quantity of these materials amounts to several thousands) supplements the Korean early modern era's historical record. However, until now these materials have received little scholarly attention from researchers except for a few historians of missionary work between Korea and America, or of Korean modern medicine. I intended to use these materials to suggest a new perspective on the study of Korean Gaehwagi. Allen, along with John W. Heron, who came to Seoul on June 21st 1885, treated about 10,460 Korean patients in the first year of the opening of JeJungWon. They made "the first annual report of the Korean Government Hospital". This report explained how Allen and Heron regarded and treated Korean patients. Allen's diaries, letters and other writings offer a realistic view of how the western people actually recognized the Korean people at that time. As a western doctor, Allen had an ambivalent attitude toward Korean medical concepts

  19. [A study on Horace N. Allen's medicine and recognition of Korean body].

    PubMed

    Lee, Young Ah

    2011-12-31

    Je Jung Won was the first modern-style Government hospital built by the Korean King Ko-Jong in April 1885, and it was the medical missionary Horace Newton Allen(1858~1932) who made one of the greatest contributions to the establishment of the hospital. Allen was an American missionary. He graduated from Ohio Wesleyan University with a degree in theology in 1881, and completed one-yearcourse at Miami Medical College. In Korea and America he worked as a physician, a missionary, an American diplomatic minister to Korea and a Korean minister's secretary to America. While acting as a mediator between Korea and America, he knew and recorded the domestic and foreign situation of Korea during Gaehwagi(the civilized and enlightened age). Thus to study him is to understand Korea's Gaehwagi as well as to research American medical missionaries. During his stay in Korea(1884~1905), Allen steadily wrote diaries and letters about Korean politics, diplomacy, society, culture, and medicine. Thus his public/private record through diaries and letters(the quantity of these materials amounts to several thousands) supplements the Korean early modern era's historical record. However, until now these materials have received little scholarly attention from researchers except for a few historians of missionary work between Korea and America, or of Korean modern medicine. I intended to use these materials to suggest a new perspective on the study of Korean Gaehwagi. Allen, along with John W. Heron, who came to Seoul on June 21st 1885, treated about 10,460 Korean patients in the first year of the opening of JeJungWon. They made "the first annual report of the Korean Government Hospital". This report explained how Allen and Heron regarded and treated Korean patients. Allen's diaries, letters and other writings offer a realistic view of how the western people actually recognized the Korean people at that time. As a western doctor, Allen had an ambivalent attitude toward Korean medical concepts

  20. BNL ATLAS Grid Computing

    ScienceCinema

    Michael Ernst

    2016-07-12

    As the sole Tier-1 computing facility for ATLAS in the United States and the largest ATLAS computing center worldwide Brookhaven provides a large portion of the overall computing resources for U.S. collaborators and serves as the central hub for storing,

  1. BNL ATLAS Grid Computing

    SciTech Connect

    Michael Ernst

    2008-10-02

    As the sole Tier-1 computing facility for ATLAS in the United States and the largest ATLAS computing center worldwide Brookhaven provides a large portion of the overall computing resources for U.S. collaborators and serves as the central hub for storing,

  2. ATLAS ACCEPTANCE TEST

    SciTech Connect

    Cochrane, J. C. , Jr.; Parker, J. V.; Hinckley, W. B.; Hosack, K. W.; Mills, D.; Parsons, W. M.; Scudder, D. W.; Stokes, J. L.; Tabaka, L. J.; Thompson, M. C.; Wysocki, Frederick Joseph; Campbell, T. N.; Lancaster, D. L.; Tom, C. Y.

    2001-01-01

    The acceptance test program for Atlas, a 23 MJ pulsed power facility for use in the Los Alamos High Energy Density Hydrodynamics program, has been completed. Completion of this program officially releases Atlas from the construction phase and readies it for experiments. Details of the acceptance test program results and of machine capabilities for experiments will be presented.

  3. Language Industries Atlas.

    ERIC Educational Resources Information Center

    Hearn, P. M., Ed.; Button, D. F., Ed.

    This atlas describes the activities of public and private organizations that create the infrastructure within which languages are able to develop and interact in the European Community (EC). It contains over 1,000 descriptions of activities that play a role in shaping the language industries, from a user or provider perspective. The atlas is…

  4. Out-of-atlas likelihood estimation using multi-atlas segmentation

    PubMed Central

    Asman, Andrew J.; Chambless, Lola B.; Thompson, Reid C.; Landman, Bennett A.

    2013-01-01

    Purpose: Multi-atlas segmentation has been shown to be highly robust and accurate across an extraordinary range of potential applications. However, it is limited to the segmentation of structures that are anatomically consistent across a large population of potential target subjects (i.e., multi-atlas segmentation is limited to “in-atlas” applications). Herein, the authors propose a technique to determine the likelihood that a multi-atlas segmentation estimate is representative of the problem at hand, and, therefore, identify anomalous regions that are not well represented within the atlases. Methods: The authors derive a technique to estimate the out-of-atlas (OOA) likelihood for every voxel in the target image. These estimated likelihoods can be used to determine and localize the probability of an abnormality being present on the target image. Results: Using a collection of manually labeled whole-brain datasets, the authors demonstrate the efficacy of the proposed framework on two distinct applications. First, the authors demonstrate the ability to accurately and robustly detect malignant gliomas in the human brain—an aggressive class of central nervous system neoplasms. Second, the authors demonstrate how this OOA likelihood estimation process can be used within a quality control context for diffusion tensor imaging datasets to detect large-scale imaging artifacts (e.g., aliasing and image shading). Conclusions: The proposed OOA likelihood estimation framework shows great promise for robust and rapid identification of brain abnormalities and imaging artifacts using only weak dependencies on anomaly morphometry and appearance. The authors envision that this approach would allow for application-specific algorithms to focus directly on regions of high OOA likelihood, which would (1) reduce the need for human intervention, and (2) reduce the propensity for false positives. Using the dual perspective, this technique would allow for algorithms to focus on

  5. Multi-Atlas Based Representations for Alzheimer’s Disease Diagnosis

    PubMed Central

    Min, Rui; Wu, Guorong; Cheng, Jian; Wang, Qian; Shen, Dinggang

    2014-01-01

    Brain morphometry based classification from magnetic resonance (MR) acquisitions has been widely investigated in the diagnosis of Alzheimer’s disease (AD) and its prodromal stage, i.e., mild cognitive impairment (MCI). In the literature, a morphometric representation of brain structures is obtained by spatial normalization of each image into a common space (i.e., a pre-defined atlas) via non-linear registration, thus the corresponding regions in different brains can be compared. However, representations generated from one single atlas may not be sufficient to reveal the underlying anatomical differences between the groups of disease-affected patients and normal controls (NC). In this article, we propose a different methodology, namely the multi-atlas based morphometry, which measures morphometric representations of the same image in different spaces of multiple atlases. Representations generated from different atlases can thus provide the complementary information to discriminate different groups, and also reduce the negative impacts from registration errors. Specifically, each studied subject is registered to multiple atlases, where adaptive regional features are extracted. Then, all features from different atlases are jointly selected by a correlation and relevance based scheme, followed by final classification with the support vector machine (SVM). We have evaluated the proposed method on 459 subjects (97 AD, 117 progressive-MCI (p-MCI), 117 stable-MCI (s-MCI), and 128 NC) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database, and achieved 91.64% for AD/NC classification and 72.41% for p-MCI/s-MCI classification. Our results clearly demonstrate that the proposed multi-atlas based method can significantly outperform the previous single-atlas based methods. PMID:24753060

  6. National Atlas maps

    USGS Publications Warehouse

    ,

    1991-01-01

    The National Atlas of the United States of America was published by the U.S. Geological Survey in 1970. Its 765 maps and charts are on 335 14- by 19-inch pages. Many of the maps span facing pages. It's worth a quick trip to the library just to leaf through all 335 pages of this book. Rapid scanning of its thematic maps yields rich insights to the geography of issues of continuing national interest. On most maps, the geographic patterns are still valid, though the data are not current. The atlas is out of print, but many of its maps can be purchased separately. Maps that span facing pages in the atlas are printed on one sheet. The maps dated after 1970 are either revisions of original atlas maps, or new maps published in atlas format. The titles of the separate maps are listed here.

  7. Diabetes Interactive Atlas.

    PubMed

    Kirtland, Karen A; Burrows, Nilka R; Geiss, Linda S

    2014-02-06

    The Diabetes Interactive Atlas is a recently released Web-based collection of maps that allows users to view geographic patterns and examine trends in diabetes and its risk factors over time across the United States and within states. The atlas provides maps, tables, graphs, and motion charts that depict national, state, and county data. Large amounts of data can be viewed in various ways simultaneously. In this article, we describe the design and technical issues for developing the atlas and provide an overview of the atlas' maps and graphs. The Diabetes Interactive Atlas improves visualization of geographic patterns, highlights observation of trends, and demonstrates the concomitant geographic and temporal growth of diabetes and obesity.

  8. A Glimpse of Atlas

    NASA Technical Reports Server (NTRS)

    2005-01-01

    Saturn's little moon Atlas orbits Saturn between the outer edge of the A ring and the fascinating, twisted F ring. This image just barely resolves the disk of Atlas, and also shows some of the knotted structure for which the F ring is known. Atlas is 32 kilometers (20 miles) across.

    The bright outer edge of the A ring is overexposed here, but farther down the image several bright ring features can be seen.

    The image was taken in visible light with the Cassini spacecraft narrow-angle camera on April 25, 2005, at a distance of approximately 2.4 million kilometers (1.5 million miles) from Atlas and at a Sun-Atlas-spacecraft, or phase, angle of 60 degrees. Resolution in the original image was 14 kilometers (9 miles) per pixel.

  9. Automatic brain segmentation in rhesus monkeys

    NASA Astrophysics Data System (ADS)

    Styner, Martin; Knickmeyer, Rebecca; Joshi, Sarang; Coe, Christopher; Short, Sarah J.; Gilmore, John

    2007-03-01

    Many neuroimaging studies are applied to primates as pathologies and environmental exposures can be studied in well-controlled settings and environment. In this work, we present a framework for both the semi-automatic creation of a rhesus monkey atlas and a fully automatic segmentation of brain tissue and lobar parcellation. We determine the atlas from training images by iterative, joint deformable registration into an unbiased average image. On this atlas, probabilistic tissue maps and a lobar parcellation. The atlas is then applied via affine, followed by deformable registration. The affinely transformed atlas is employed for a joint T1/T2 based tissue classification. The deformed atlas parcellation masks the tissue segmentations to define the parcellation. Other regional definitions on the atlas can also straightforwardly be used as segmentation. We successfully built average atlas images for the T1 and T2 datasets using a developmental training datasets of 18 cases aged 16-34 months. The atlas clearly exhibits an enhanced signal-to-noise ratio compared to the original images. The results further show that the cortical folding variability in our data is highly limited. Our segmentation and parcellation procedure was successfully re-applied to all training images, as well as applied to over 100 additional images. The deformable registration was able to identify corresponding cortical sulcal borders accurately. Even though the individual methods used in this segmentation framework have been applied before on human data, their combination is novel, as is their adaptation and application to rhesus monkey MRI data. The reduced variability present in the primate data results in a segmentation pipeline that exhibits high stability and anatomical accuracy.

  10. Subcortical structure segmentation using probabilistic atlas priors

    NASA Astrophysics Data System (ADS)

    Gouttard, Sylvain; Styner, Martin; Joshi, Sarang; Smith, Rachel G.; Cody Hazlett, Heather; Gerig, Guido

    2007-03-01

    The segmentation of the subcortical structures of the brain is required for many forms of quantitative neuroanatomic analysis. The volumetric and shape parameters of structures such as lateral ventricles, putamen, caudate, hippocampus, pallidus and amygdala are employed to characterize a disease or its evolution. This paper presents a fully automatic segmentation of these structures via a non-rigid registration of a probabilistic atlas prior and alongside a comprehensive validation. Our approach is based on an unbiased diffeomorphic atlas with probabilistic spatial priors built from a training set of MR images with corresponding manual segmentations. The atlas building computes an average image along with transformation fields mapping each training case to the average image. These transformation fields are applied to the manually segmented structures of each case in order to obtain a probabilistic map on the atlas. When applying the atlas for automatic structural segmentation, an MR image is first intensity inhomogeneity corrected, skull stripped and intensity calibrated to the atlas. Then the atlas image is registered to the image using an affine followed by a deformable registration matching the gray level intensity. Finally, the registration transformation is applied to the probabilistic maps of each structures, which are then thresholded at 0.5 probability. Using manual segmentations for comparison, measures of volumetric differences show high correlation with our results. Furthermore, the dice coefficient, which quantifies the volumetric overlap, is higher than 62% for all structures and is close to 80% for basal ganglia. The intraclass correlation coefficient computed on these same datasets shows a good inter-method correlation of the volumetric measurements. Using a dataset of a single patient scanned 10 times on 5 different scanners, reliability is shown with a coefficient of variance of less than 2 percents over the whole dataset. Overall, these validation

  11. Measuring specific receptor binding of a PET radioligand in human brain without pharmacological blockade: The genomic plot.

    PubMed

    Veronese, Mattia; Zanotti-Fregonara, Paolo; Rizzo, Gaia; Bertoldo, Alessandra; Innis, Robert B; Turkheimer, Federico E

    2016-04-15

    PET studies allow in vivo imaging of the density of brain receptor species. The PET signal, however, is the sum of the fraction of radioligand that is specifically bound to the target receptor and the non-displaceable fraction (i.e. the non-specifically bound radioligand plus the free ligand in tissue). Therefore, measuring the non-displaceable fraction, which is generally assumed to be constant across the brain, is a necessary step to obtain regional estimates of the specific fractions. The nondisplaceable binding can be directly measured if a reference region, i.e. a region devoid of any specific binding, is available. Many receptors are however widely expressed across the brain, and a true reference region is rarely available. In these cases, the nonspecific binding can be obtained after competitive pharmacological blockade, which is often contraindicated in humans. In this work we introduce the genomic plot for estimating the nondisplaceable fraction using baseline scans only. The genomic plot is a transformation of the Lassen graphical method in which the brain maps of mRNA transcripts of the target receptor obtained from the Allen brain atlas are used as a surrogate measure of the specific binding. Thus, the genomic plot allows the calculation of the specific and nondisplaceable components of radioligand uptake without the need of pharmacological blockade. We first assessed the statistical properties of the method with computer simulations. Then we sought ground-truth validation using human PET datasets of seven different neuroreceptor radioligands, where nonspecific fractions were either obtained separately using drug displacement or available from a true reference region. The population nondisplaceable fractions estimated by the genomic plot were very close to those measured by actual human blocking studies (mean relative difference between 2% and 7%). However, these estimates were valid only when mRNA expressions were predictive of protein levels (i

  12. Measuring specific receptor binding of a PET radioligand in human brain without pharmacological blockade: The genomic plot.

    PubMed

    Veronese, Mattia; Zanotti-Fregonara, Paolo; Rizzo, Gaia; Bertoldo, Alessandra; Innis, Robert B; Turkheimer, Federico E

    2016-04-15

    PET studies allow in vivo imaging of the density of brain receptor species. The PET signal, however, is the sum of the fraction of radioligand that is specifically bound to the target receptor and the non-displaceable fraction (i.e. the non-specifically bound radioligand plus the free ligand in tissue). Therefore, measuring the non-displaceable fraction, which is generally assumed to be constant across the brain, is a necessary step to obtain regional estimates of the specific fractions. The nondisplaceable binding can be directly measured if a reference region, i.e. a region devoid of any specific binding, is available. Many receptors are however widely expressed across the brain, and a true reference region is rarely available. In these cases, the nonspecific binding can be obtained after competitive pharmacological blockade, which is often contraindicated in humans. In this work we introduce the genomic plot for estimating the nondisplaceable fraction using baseline scans only. The genomic plot is a transformation of the Lassen graphical method in which the brain maps of mRNA transcripts of the target receptor obtained from the Allen brain atlas are used as a surrogate measure of the specific binding. Thus, the genomic plot allows the calculation of the specific and nondisplaceable components of radioligand uptake without the need of pharmacological blockade. We first assessed the statistical properties of the method with computer simulations. Then we sought ground-truth validation using human PET datasets of seven different neuroreceptor radioligands, where nonspecific fractions were either obtained separately using drug displacement or available from a true reference region. The population nondisplaceable fractions estimated by the genomic plot were very close to those measured by actual human blocking studies (mean relative difference between 2% and 7%). However, these estimates were valid only when mRNA expressions were predictive of protein levels (i

  13. Recent radiation belt discoveries from the Van Allen Probes mission, outstanding questions, and future opportunities

    NASA Astrophysics Data System (ADS)

    Reeves, Geoffrey; Spence, Harlan

    The twin NASA Van Allen Probes satellites (formerly called Radiation Belt Storm Probes) were launched August 30, 2012 into geosynchronous transfer type orbits. The Van Allen Probes satellites host an extensive package of fields and particle instruments that provide unprecedented resolution and insensitivity to penetrating backgrounds needed to resolve among competing physical processes. The satellites were launched with an apogee near dawn. The apogee precesses Eastward taking two years to pass through all local times. The two satellites have slightly different orbital periods allowing the satellites to lap one another. This lapping provides a variety of configurations with the satellites sometimes closely separated in space and time and sometimes measuring two parts of the inner magnetosphere simultaneously. In this paper we will present some highlights of discoveries from the Van Allen Probes mission to date. Among those are: observations of the acceleration of relativistic electrons by VLF chorus waves; some unexpected occurrence of chorus waves; resonant pitch angle scattering of relativistic electrons both in those events that lead to loss and those that don’t; observations of drift resonant interactions of relativistic and sub-relativistic electrons with global ULF waves; the critical role that the sub-relativistic seed population plays in controlling radiation belt response and how substorm injections produce those seed populations; and the remarkable advances that have been made in 3D modeling of radiation belt structure and dynamics. We will also discuss the many outstanding questions that remain (as well as new questions that have arisen) and consider the remarkable opportunities that will be available thanks to new missions anticipated in the near future.

  14. Magnetohydrodynamic modeling of three Van Allen Probes storms in 2012 and 2013

    NASA Astrophysics Data System (ADS)

    Paral, J.; Hudson, M. K.; Kress, B. T.; Wiltberger, M. J.; Wygant, J. R.; Singer, H. J.

    2015-08-01

    Coronal mass ejection (CME)-shock compression of the dayside magnetopause has been observed to cause both prompt enhancement of radiation belt electron flux due to inward radial transport of electrons conserving their first adiabatic invariant and prompt losses which at times entirely eliminate the outer zone. Recent numerical studies suggest that enhanced ultra-low frequency (ULF) wave activity is necessary to explain electron losses deeper inside the magnetosphere than magnetopause incursion following CME-shock arrival. A combination of radial transport and magnetopause shadowing can account for losses observed at radial distances into L = 4.5, well within the computed magnetopause location. We compare ULF wave power from the Electric Field and Waves (EFW) electric field instrument on the Van Allen Probes for the 8 October 2013 storm with ULF wave power simulated using the Lyon-Fedder-Mobarry (LFM) global magnetohydrodynamic (MHD) magnetospheric simulation code coupled to the Rice Convection Model (RCM). Two other storms with strong magnetopause compression, 8-9 October 2012 and 17-18 March 2013, are also examined. We show that the global MHD model captures the azimuthal magnetosonic impulse propagation speed and amplitude observed by the Van Allen Probes which is responsible for prompt acceleration at MeV energies reported for the 8 October 2013 storm. The simulation also captures the ULF wave power in the azimuthal component of the electric field, responsible for acceleration and radial transport of electrons, at frequencies comparable to the electron drift period. This electric field impulse has been shown to explain observations in related studies (Foster et al., 2015) of electron acceleration and drift phase bunching by the Energetic Particle, Composition, and Thermal Plasma Suite (ECT) instrument on the Van Allen Probes.

  15. Evaluation of effects of groundwater withdrawals at the proposed Allen combined-cycle combustion turbine plant, Shelby County, Tennessee

    USGS Publications Warehouse

    Haugh, Connor J.

    2016-08-10

    The Mississippi Embayment Regional Aquifer Study groundwater-flow model was used to simulate the potential effects of future groundwater withdrawals at the proposed Allen combined-cycle combustion turbine plant in Shelby County, Tennessee. The scenario used in the simulation consisted of a 30-year average withdrawal period followed by a 30-day maximum withdrawal period. Effects of withdrawals at the Allen plant site on the Mississippi embayment aquifer system were evaluated by comparing the difference in simulated water levels in the aquifers at the end of the 30-year average withdrawal period and at the end of the scenario to a base case without the Allen combined-cycle combustion turbine plant withdrawals. Simulated potentiometric surface declines in the Memphis aquifer at the Allen plant site were about 7 feet at the end of the 30-year average withdrawal period and 11 feet at the end of the scenario. The affected area of the Memphis aquifer at the Allen plant site as delineated by the 4-foot potentiometric surface-decline contour was 2,590 acres at the end of the 30-year average withdrawal period and 11,380 acres at the end of the scenario. Simulated declines in the underlying Fort Pillow aquifer and overlying shallow aquifer were both less than 1 foot at the end of the 30-year average withdrawal period and the end of the scenario.

  16. Evaluation of effects of groundwater withdrawals at the proposed Allen combined-cycle combustion turbine plant, Shelby County, Tennessee

    USGS Publications Warehouse

    Haugh, Connor J.

    2016-01-01

    The Mississippi Embayment Regional Aquifer Study groundwater-flow model was used to simulate the potential effects of future groundwater withdrawals at the proposed Allen combined-cycle combustion turbine plant in Shelby County, Tennessee. The scenario used in the simulation consisted of a 30-year average withdrawal period followed by a 30-day maximum withdrawal period. Effects of withdrawals at the Allen plant site on the Mississippi embayment aquifer system were evaluated by comparing the difference in simulated water levels in the aquifers at the end of the 30-year average withdrawal period and at the end of the scenario to a base case without the Allen combined-cycle combustion turbine plant withdrawals. Simulated potentiometric surface declines in the Memphis aquifer at the Allen plant site were about 7 feet at the end of the 30-year average withdrawal period and 11 feet at the end of the scenario. The affected area of the Memphis aquifer at the Allen plant site as delineated by the 4-foot potentiometric surface-decline contour was 2,590 acres at the end of the 30-year average withdrawal period and 11,380 acres at the end of the scenario. Simulated declines in the underlying Fort Pillow aquifer and overlying shallow aquifer were both less than 1 foot at the end of the 30-year average withdrawal period and the end of the scenario.

  17. The Flux and Energy Spectra of the Protons in the Inner Van Allen Belt

    NASA Technical Reports Server (NTRS)

    Naugle, John E.; Kniffen, Donald A.

    1961-01-01

    A cylindrical stack of G-5 nuclear emulsions housed in the payload section of a four-stage research rocket was flown into the northern edge of the inner Van Allen belt on September 19, 1960. The experimental design permitted, for the first time, measurements of the particle fluxes and energy spectra as functions of position along the rocket trajectory. Eight points along the trajectory have been selected for analysis. Results are presented herein for three of these points, and they are discussed in the light of various theories on the trapped radiation.

  18. Science Highlights from the RBSP-ECT Particle Instrument Suite on NASA's Van Allen Probes Mission

    NASA Astrophysics Data System (ADS)

    Spence, Harlan

    2014-05-01

    The NASA Van Allen Probes mission includes an instrument suite known as the Radiation Belt Storm Probes (RBSP) - Energetic Particle, Composition, and Thermal Plasma (ECT) suite. RBSP-ECT contains a well-proven complement of particle instruments to ensure the highest quality measurements ever made in the radiation belts and the inner magnetosphere. The coordinated RBSP-ECT particle measurements, analyzed in combination with fields and waves observations and state of-the-art theory and modeling, provide new understanding on the acceleration, global distribution, and variability of radiation belt electrons and ions, key science objectives of NASA's Living With a Star program and the Van Allen Probes mission. The RBSP-ECT suite consists of three highly-coordinated instruments: the Helium Oxygen Proton Electron (HOPE) spectrometer, the Magnetic Electron Ion Spectrometer (MagEIS), and the Relativistic Electron Proton Telescope (REPT). Collectively these three instrument types cover comprehensively the full electron and ion spectra from one eV to 10's of MeV with sufficient energy resolution, pitch angle coverage and resolution, and with composition measurements in the critical energy range up to 50 keV and also from a few to 50 MeV/nucleon. All three instruments are based on measurement techniques proven in the radiation belts, then optimized to provide unambiguous separation of ions and electrons and clean energy responses even in the presence of extreme penetrating background environments. In this presentation, we summarize overall ECT science goals and then show scientific results derived from the ECT suite on the dual Van Allen Probes spacecraft to date. Mission operations began only in late October 2012, and we have now achieved significant results. Results presented here will include substantial progress toward resolving primary Van Allen Probes science targets, such as: the relative role of localized acceleration versus transport-generated particle acceleration

  19. Early Science Results From the NASA Van Allen Probes Mission RBSP-ECT Instrument Suite

    NASA Astrophysics Data System (ADS)

    Spence, Harlan; Reeves, Geoff; Rbspect Team

    2013-04-01

    The NASA Van Allen Probes mission includes an instrument suite known as the Radiation Belt Storm Probes (RBSP) - Energetic Particle, Composition, and Thermal Plasma (ECT) suite. RBSP-ECT contains a well-proven complement of particle instruments to ensure the highest quality measurements ever made in the radiation belts and the inner magnetosphere. The coordinated RBSP-ECT particle measurements, analyzed in combination with fields and waves observations and state of-the-art theory and modeling, provide new understanding on the acceleration, global distribution, and variability of radiation belt electrons and ions, key science objectives of NASA's Living With a Star program and the Van Allen Probes mission. The RBSP-ECT suite consists of three highly-coordinated instruments: the Helium Oxygen Proton Electron (HOPE) spectrometer, the Magnetic Electron Ion Spectrometer (MagEIS), and the Relativistic Electron Proton Telescope (REPT). Collectively these three instrument types cover comprehensively the full electron and ion spectra from one eV to 10's of MeV with sufficient energy resolution, pitch angle coverage and resolution, and with composition measurements in the critical energy range up to 50 keV and also from a few to 50 MeV/nucleon. All three instruments are based on measurement techniques proven in the radiation belts, then optimized to provide unambiguous separation of ions and electrons and clean energy responses even in the presence of extreme penetrating background environments. In this presentation, we summarize overall ECT science goals and then show early scientific results derived from the ECT suite on the dual Van Allen Probes spacecraft. Mission operations began only in late October 2012, but we have already achieved significant early results. Results presented here will include substantial progress toward resolving primary Van Allen Probes science targets, such as: the relative role of localized acceleration versus transport-generated particle

  20. Catalytic enantioselective protoboration of disubstituted allenes. Access to alkenylboron compounds in high enantiomeric purity.

    PubMed

    Jang, Hwanjong; Jung, Byunghyuck; Hoveyda, Amir H

    2014-09-01

    Proto-boryl additions to 1,1-disubstituted allenes in the presence of 1.0-5.0 mol % of chiral NHC-Cu complexes, B2(pin)2, and t-BuOH proceed to afford alkenyl-B(pin) products in up to 98% yield, >98:2 site selectivity, and 98:2 er. The enantiomerically enriched alkenylboron products can be converted to otherwise difficult-to-access alkenyl bromides, methyl ketones or carboxylic acids. What's more, the corresponding boronic acids may be used in highly stereoselective NHC-Cu-catalyzed allylic substitution reactions. PMID:25153792

  1. MEDICAL MANAGEMENT OF LEIOMYOMATA AND SUSPECTED ENDOMETRIOSIS IN AN ALLEN'S SWAMP MONKEY (ALLENOPITHECUS NIGROVIRIDUS).

    PubMed

    Jafarey, Yousuf S; Hanley, Christopher S; Berlinski, Ric A; Warner, Connie; Armstrong, Anthony

    2015-12-01

    A 13-yr-old female nulliparous Allen's swamp monkey (Allenopitchecus nigroviridis) presented with intermittent excessive vaginal bleeding, cyclical lethargy, and a history of irregular menstrual cycles. Abdominal ultrasonography revealed a subjectively thickened, irregular endometrium, multiple leiomyomata (uterine fibroids), and bilateral anechoic foci on the ovaries. Treatment was initiated with leuprolide acetate i.m. monthly for 6 mo. Recheck ultrasound at 3 mo showed a decrease in leiomyoma diameter and no evidence of active follicles on the ovaries. Eleven months following completion of treatment, clinical signs recurred and the animal was treated with a deslorelin implant. Since implant placement, no vaginal bleeding has been noted. PMID:26667550

  2. Effect of the orbital debris environment on the high-energy Van Allen proton belt

    NASA Technical Reports Server (NTRS)

    Konradi, Andrei

    1988-01-01

    The lifetimes of high-energy (greater than 55 MeV) protons in the Van Allen radiation belt are calculated, assuming that in time the protons will collide with and be absorbed by particulate orbiting material. The calculations are based on the NASA/DoD Civil Needs Database for orbital debris (Gaines, 1966) and moderate assumptions of future space traffic. It is found that the lifetimes of high-energy protons below 1500 km will decrease, leading to a noticeable redution in their fluxes.

  3. Accounting for Diradical Character through DFT. The Case of Vinyl Allene Oxide Rearrangement.

    PubMed

    López, Roberto Villar; Faza, Olalla Nieto; López, Carlos Silva

    2015-11-01

    The transformation of vinyl allene oxides into cyclopentenones is key to the biosynthesis of a number of hormone-like molecules in plants. Two competitive paths are generally accepted for this transformation: a concerted SN2-like mechanism and a stepwise path with a diradical oxyallyl intermediate. Recently, a new stepwise closed-shell path has been proposed that circumvents the key oxyallyl intermediate. In this work, we conduct a thorough computational investigation, including dynamic effects, to identify the most likely mechanism for this transformation.

  4. Regioisomeric allene dimer formation by the reaction of tetraarylbutatrienes with tetracyanoethene.

    PubMed

    Ueta, Shoko; Hida, Kazuo; Nishiuchi, Masaki; Kawamura, Yasuhiko

    2014-05-01

    The reaction of tetraarylbutatrienes (tetraaryl[3]cumulenes) with tetracyanoethene (TCNE), a strong electron-accepting molecule, at room temperature yielded novel four-membered ring compounds (head-to-tail unsymmetrically substituted diarylallene dimers) by [2 + 2] cycloaddition of the central C=C bond of the butatrienes. This reaction proceeded through a head-to-head symmetrically substituted diarylallene dimer intermediate. Unsymmetrical butatriene also formed a small amount of another head-to-tail dimer. Although the allene dimer is stable in nonpolar solvents, it converts to other bicyclic and tricyclic compounds in MeOH or CH3CN at room temperature.

  5. Internet-enabled high-resolution brain mapping and virtual microscopy.

    PubMed

    Mikula, Shawn; Trotts, Issac; Stone, James M; Jones, Edward G

    2007-03-01

    Virtual microscopy involves the conversion of histological sections mounted on glass microscope slides to high-resolution digital images. Virtual microscopy offers several advantages over traditional microscopy, including remote viewing and data sharing, annotation, and various forms of data mining. We describe a method utilizing virtual microscopy for generation of internet-enabled, high-resolution brain maps and atlases. Virtual microscopy-based digital brain atlases have resolutions approaching 100,000 dpi, which exceeds by three or more orders of magnitude resolutions obtainable in conventional print atlases, MRI, and flat-bed scanning. Virtual microscopy-based digital brain atlases are superior to conventional print atlases in five respects: (1) resolution, (2) annotation, (3) interaction, (4) data integration, and (5) data mining. Implementation of virtual microscopy-based digital brain atlases is located at BrainMaps.org, which is based on more than 10 million megapixels (35 terabytes) of scanned images of serial sections of primate and non-primate brains with a resolution of 0.46 microm/pixel (55,000 dpi). The method can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. Online tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level and can facilitate large-scale connectional tracing, histochemical, and stereological analyses. PMID:17229579

  6. The Millennium Star Atlas

    NASA Astrophysics Data System (ADS)

    Sinnott, R. W.

    1997-08-01

    Derived from Hipparcos and Tycho observations, the Millennium Star Atlas is a set of 1548 charts covering the entire sky to about magnitude 11. It stands apart from all previous printed atlases in completeness to magnitude 10 and in uniformity around the sky. The generous chart scale has made possible a number of innovations never before seen in a star atlas: arrows on high-proper-motion stars, double-star ticks conveying separation and position angle for a specific modern epoch, distance labels for nearby stars, and variable stars coded by amplitude, period, and type. Among the nonstellar objects plotted, more than 8000 galaxies are shown with aspect ratio and orientation.

  7. Brain spatial normalization.

    PubMed

    Bug, William; Gustafson, Carl; Shahar, Allon; Gefen, Smadar; Fan, Yingli; Bertrand, Louise; Nissanov, Jonathan

    2007-01-01

    Neuroanatomical informatics, a subspecialty of neuroinformatics, focuses on technological solutions to neuroimage database access. Its current main goal is an image-based query system that is able to retrieve imagery based on anatomical location. Here, we describe a set of tools that collectively form such a solution for sectional material and that are available to investigators to use on their own data sets. The system accepts slide images as input and yields a matrix of transformation parameters that map each point on the input image to a standardized 3D brain atlas. In essence, this spatial normalization makes the atlas a spatial indexer from which queries can be issued simply by specifying a location on the reference atlas. Our objective here is to familiarize potential users of the system with the steps required of them as well as steps that take place behind the scene. We detail the capabilities and the limitations of the current implementation and briefly describe the enhancements planned for the near future.

  8. Catalyst-Dependent Stereodivergent and Regioselective Synthesis of Indole-Fused Heterocycles through Formal Cycloadditions of Indolyl-Allenes.

    PubMed

    Mei, Liang-Yong; Wei, Yin; Tang, Xiang-Ying; Shi, Min

    2015-07-01

    Stereo- and regioselective construction of poly-heterocycles, especially those with several contiguous stereocenters, is still a challenge. In this paper, catalyst-dependent stereodivergent and regioselective synthesis of indole-fused heterocycles through formal cycloadditions of indolyl-allenes has been developed. The reaction features total reversion of an all-carbon quaternary stereocenter when a gold or platinum complex was employed as the catalyst through [3 + 2] cycloaddition of allene with indole, affording different diazabenzo[a]cyclopenta[cd]azulenes as epimers, respectively. In addition, in the presence of IPrAuCl and AgNTf2, highly regioselective exo-type [2 + 2] cycloaddition was observed, in which allene served as a 2C synthon. This methodology provides a simple and straightforward approach for the construction of indole-fused tricyclic systems under mild conditions in an atom-economical way.

  9. Soot formation in pyrolysis of acetylene, allene and 1,3-butadiene

    NASA Technical Reports Server (NTRS)

    Frenklach, M.; Durgaprasad, M. B.; Matula, R. A.; Taki, S.

    1983-01-01

    The formation of soot behind reflected shock waves in argon-diluted mixtures of acetylene, allene, and 1,3-butadiene was investigated by monitoring the attenuation of a laser beam in both the visible (632.8 nm) and the infrared (3.39 microns) regions of the spectrum. The experiments utilized temperatures ranging from 1500-3100 K, reflected shock pressures of 0.3-7.0 bar, and total carbon atom concentrations of 2-20 x 10 to the 17th atoms/cu cm. A bell-shaped dependence of soot yield on temperature was observed during the pyrolysis of all three compounds, which was similar to that previously found for toluene. For acetylene, the decrese in total pressure was found to shift the soot bell to higher temperatures with a significant increase in the maximum soot yield. A computer simulation for acetylene pyrolysis suggested that the reactions between C2H3, C4H3, and C4H4 may be those which lead to the formation of aromatic structures. In addition, it was found that soot is formed much faster and in much larger quantities from allene than from 1,3-butadiene.

  10. Ion Spectral Structures Observed by the Van Allen Probes and Cluster

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Luo, H.; Kistler, L. M.; Spence, H. E.; Larsen, B.; Skoug, R. M.; Funsten, H. O.; Reeves, G. D.

    2014-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have revealed single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). In this study we also include signatures of new types of ion structure, namely "trunk-like" and "tusk-like" structures. All the ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Multi-spacecraft analysis of these structures is important to understand their spatial distribution and temporal evolution. Mass spectrometers onboard Cluster (in a polar orbit) and the Van Allen Probes (in an equatorial orbit) measure energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of the ion structures, using >1-year measurements from the two missions during the Van Allen Probes era. The results provide important details about the spatial distribution (dependence on geocentric distance and magnetic local time), spectral features of the structures (e.g., characteristic energy and differences among species), and geomagnetic and solar wind conditions under which these structures occur.

  11. Marine ecological-risk assessment pilot study for Allen Harbor, Narragansett Bay, Rhode Island. Professional paper

    SciTech Connect

    Johnston, R.K.; Munns, W.R.; Mueller, C.; Nelson, W.G.; Pesch, G.G.

    1992-01-01

    An ecological risk assessment framework was applied to characterize aquatic risks associated with hazardous waste disposal at Naval Construction Battalion Center (NCBC) Davisville, Rhode Island. An initial screening phase (I) assessed exposure and related that exposure to toxicological endpoints for bivalves, amphipods, sea urchins, and biomarker assays. Results showed little evidence of major contamination in sediments or tissues except for relatively high levels of polychlorinated biphenols (PBC), butyltins compounds (TBT), and fecal coliforms observed in Allen Harbor. Effects were detected in mussel physiology, sea urchin fertilization and development, biomarker responses, and soft shell clam histology. Possible sources of contamination and toxicity from the landfill leachate, surface runoff, and recreational boating were examined using a temporaland spatial sampling scheme. Chemical and toxicological information obtained implicated all three sources as affecting Allen Harbor water quality. Laboratory bioassays of landfill exposure media, employing a variety of marine species using acute and chronic endpoints, are being used to provide data for the development of an exposure-response model for risk to the marine environment. The model will define current risk and provide an interpretive framework for long-term monitoring.

  12. Van Allen Probes RBSPICE Observations of the March 2015 Solar Storm

    NASA Astrophysics Data System (ADS)

    Manweiler, J. W.; Patterson, J. D.; Gerrard, A. J.; Gkioulidou, M.; Mitchell, D. G.; Lanzerotti, L. J.

    2015-12-01

    The Van Allen Probes Radiation Belt Storm Probes Ion Composition Experiment (RBSPICE) instrument provides the ability to measure the energetic particle composition of the Earth's ring current from 20 KeV to approximately 1 MeV. On March 17, 2015 a solar storm impacted the Earth with a maximum negative Dst of -232. The onset of the storm was directly observed by the RBSPICE B instrument. The RBSPICE A instrument observed the development of the storm prior to onset in one orbit and a few hours after onset on the subsequent orbit. These observations displayed a number of interesting features of the storm including an Oxygen beam, high beta plasma conditions, and multiple injections of protons, helium, and oxygen into the inner magnetosphere. Our presentation will report on the observations made from each RBSPICE instrument coupled with observations from other Van Allen Probes instruments (EMFISIS, ECT, and EFW) to provide a complete picture of the impact of this storm on the Earth's inner magnetosphere.

  13. Simultaneous Observation of Plasma Waves Detected by the Van Allen Probes Spacecraft During Close Spacecraft Separations

    NASA Astrophysics Data System (ADS)

    Hospodarsky, George; Santolik, Ondrej; Averkamp, Terrance; Bounds, Scott; Kurth, William; Kletzing, Craig; Wygant, John; Bonnell, John

    2014-05-01

    The twin Van Allen Probe spacecraft launched in August 2012 includes the Electric and Magnetic Field Instrument Suite and Integrated Science (EMFISIS) Wave instrument that simultaneously measures three orthogonal components of the wave magnetic field and, with the support of the Electric Fields and Waves (EFW) instrument sensors, three components of the wave electric field at two locations in Earth's magnetosphere. Measuring all six wave components simultaneously allows the wave propagation parameters, such as the wave normal angle and Poynting vector, of the plasma wave emissions to be obtained. The orbit of the spacecraft are designed such that they "lap" each other roughly every 69 days, allowing observations over a range of spacecraft separations, with the closest separations on the order of 100 km. Simultaneous measurements at a range of distances between the two spacecraft provide an opportunity to investigate the scale, size and propagation characteristics of a number of plasma wave emissions associated with the Van Allen radiation belts, including whistler mode chorus. We examine these characteristics of the emissions detected by both spacecraft during separation distance of < 1000 km. Very similar small scale chorus wave packets were detected by both spacecraft when separation distances were the smallest. The similarities and differences detected by both spacecraft and their relation to separation distances will be discussed.

  14. Collier Cobb and Allen D. Hole: Geologic mentors to early soil scientists

    NASA Astrophysics Data System (ADS)

    Brevik, Eric C.

    Many influential individuals involved in the early US soil survey program were trained as geologists rather than as agronomists or soil scientists. Several geology departments served as pipelines for students interested in a career in soil survey. This paper looks at the professional history of two early mentors of these geologists turned soil surveyors and some of the students they sent on to the US soil survey and other soil science careers. Collier Cobb sent over 10 students to the soil survey starting in 1900 when US soil survey was in its infancy, including individuals of note such as Hugh H. Bennett, George N. Coffey, Williamson E. Hearn, and Thomas D. Rice. Allen D. Hole worked on soil surveys for the state of Indiana and sent over a dozen students on to US soil survey careers between 1911 and 1937, including Mark Baldwin and James Thorp. Francis Hole and Ralph McCracken, other students of Allen Hole, also went on to have distinguished soil science careers. These mentors and students clearly show the close ties that existed between soil science and geology in the United States during the early 1900s.

  15. Collier Cobb and Allen D. Hole: Geologic Mentors to Early American Soil Scientists

    NASA Astrophysics Data System (ADS)

    Brevik, E. C.

    2012-04-01

    Many influential individuals involved in the early United States soil survey program were trained as geologists rather than as agronomists or soil scientists. Several geology departments served as pipelines for students interested in a career in soil survey. This presentation looks at the professional history of two early mentors of these geologists turned soil surveyors and some of the students they sent on to the U.S. soil survey and other soil science careers. Collier Cobb (University of North Carolina) sent over 10 students to the soil survey starting in 1900 when U.S. soil survey was in its infancy, including individuals of note such as Hugh H. Bennett, George N. Coffey, Williamson E. Hearn, and Thomas D. Rice. Allen D. Hole (Earlham College, Indiana) worked on soil surveys for the state of Indiana and sent over a dozen students on to U.S. soil survey careers between 1911 and 1937, including Mark Baldwin and James Thorp. Francis Hole and Ralph McCracken, other students of Allen Hole, also went on to have distinguished soil science careers. These mentors and students clearly show the close ties that existed between soil science and geology in the United States during the early 1900s.

  16. Impacts of intense inward and outward ULF wave radial diffusion on the Van Allen belts

    NASA Astrophysics Data System (ADS)

    Mann, Ian; Ozeke, Louis; Rae, I. Jonathan; Murphy, Kyle

    2016-07-01

    During geomagnetic storms, the power in ultra-low frequency (ULF) waves can be orders of magnitude larger than that predicted by statistics determined from an entire solar cycle. This is especially true during the main phase and early recovery phase. These periods of enhanced storm-time ULF wave power can have significant impacts on the morphology and structure of the Van Allen belts. Either fast inward or outward radial diffusion can result, depending on the profiles of the electron phase space density and the outer boundary condition at the edge of the belts. Small changes in the time sequence of powerful ULF waves, and the time sequence of any magnetopause shadowing or the recovery of plamasheet sources relative to the ULF wave occurrence, have a remarkable impact on the resulting structure of the belts. The overall impact of the enhanced ULF wave power is profound, but the response can be very different depending on the available source flux in the plasmasheet. We review these impacts by examining ultra-relativistic electron dynamics during seemingly different storms during the Van Allen Probe era, including during the Baker et al. third radiation belt, and show the observed behaviour can be largely explained by differences in the time sequence of events described above.

  17. Prospects of Comparing Van Allen Probes Data with Recent Nonlinear Radiation Belt Theory

    NASA Astrophysics Data System (ADS)

    Summers, D.; Omura, Y.; Tang, R.

    2013-12-01

    We consider the prospects of comparing recently developed theory and simulations of nonlinear wave processes with Van Allen Probes observational data. Electron gyro-resonant interaction with whistler-mode chorus waves is considered to be a prime mechanism for generating relativistic electrons in Earth's outer radiation belt. Resonant pitch angle scattering by chorus can also cause significant electron precipitation loss from the inner magnetosphere. Whistler-mode waves can as well act to suppress radiation belt electron fluxes below a theoretical (Kennel-Petschek) limit. Nonlinear cyclotron resonance theory is required to analyze the nonlinear characteristics of whistler-mode wave generation and the interaction of chorus with radiation belt electrons. We discuss recently developed nonlinear theory that involves wave trapping of resonant electrons near the equator and the formation of an electron hole in the phase space. The resulting formation of a resonant current causes nonlinear growth of a wave with rising frequency. Nonlinear wave trapping plays a significant role in both the generation of whistler-mode chorus emissions and the acceleration of radiation belt electrons to relativistic energies. A fraction of radiation belt electrons can be energized extremely efficiently by special wave trapping mechanisms called "relativistic turning acceleration" and "ultra-relativistic acceleration". In this presentation we summarize the salient features of whistler-mode wave generation and these associated acceleration processes,and discuss how they can be compared with particle and wave data from the Van Allen Probes mission.

  18. Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata

    PubMed Central

    Aplasca, Andrea C.; Iverson, John B.; Welch, Mark E.; Colosimo, Giuliano

    2016-01-01

    The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations. PMID:26989628

  19. 'Trunk-like' ion structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Kistler, L. M.; Spence, H.; Wolf, R.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.; Larsen, B.; Niehof, J. T.; MacDonald, E.; Friedel, R. H.

    2013-12-01

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. In this study, we report 'trunk-like' ion structures observed in situ by the Van Allen Probes on 2 November 2012. The trunk structures are present in heavy ions but not in H+. For the particular event, ion energies in the He+ trunks, located at L = 3.7-2.6, MLT = 8.8-10.3, and MLAT = -2.0-0.03°, vary monotonically from 3.5 to 0.04 keV. It is suggested that the trunk phenomenon is due to a combination of 1) deeper ion injections from storm activity, 2) the longer charge exchange lifetimes of heavy ions than H+, 3) the separation of a narrow layer of ions around the Alfvén layer from other convecting ions, and 4) the trajectory of the Van Allen Probes (i.e., an orbital effect). Both observation analysis and numerical modeling are utilized in the study.

  20. Relativistic Electrons in the Inner Zone and Slot - Quiet Time Observations by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Blake, J. B.; Fennell, J. F.; Claudepierre, S. G.; Looper, M. D.; Mazur, J. E.; O'Brien, T. P.; Clemmons, J. H.; Baker, D. N.; Reeves, G. D.; Spence, H.; Funsten, H. O.

    2013-12-01

    The energy spectra of relativistic electrons in the inner zone and slot region are old questions dating from the early days of space research. There are two major reasons for this situation: the paucity of scientific missions traversing the inner zone and slot region at low inclination, and the technical difficulty of making relativistic electron measurements in the presence of the very energetic protons and intense fluxes of electrons with energies up to a few hundred keV that are found in the inner zone. The Van Allen Probes mission offers a new opportunity to address this problem. This mission to date has taken place during a time period of only modest geomagnetic activity with no unusual increases of the energetic electron population deep inside the magnetosphere such as the shock injection of 24 March 1991 or the Halloween storm of 2003. We began by examining observations made during some of the quieter times since launch, in late January and early February 2013. The data show that the inner zone electron fluxes indeed drop to very low intensities by several hundred keV. A major focus of this preliminary study has been a careful examination of sources of background and its removal in the electron spectrometers using several of the Van Allen probe instruments. Upper limits on the relativistic electron intensities as a function of L will be presented.

  1. An impenetrable barrier to ultrarelativistic electrons in the Van Allen radiation belts.

    PubMed

    Baker, D N; Jaynes, A N; Hoxie, V C; Thorne, R M; Foster, J C; Li, X; Fennell, J F; Wygant, J R; Kanekal, S G; Erickson, P J; Kurth, W; Li, W; Ma, Q; Schiller, Q; Blum, L; Malaspina, D M; Gerrard, A; Lanzerotti, L J

    2014-11-27

    Early observations indicated that the Earth's Van Allen radiation belts could be separated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons of moderate energy (less than about one megaelectronvolt) often populate both zones, with a deep 'slot' region largely devoid of particles between them. There is a region of dense cold plasma around the Earth known as the plasmasphere, the outer boundary of which is called the plasmapause. The two-belt radiation structure was explained as arising from strong electron interactions with plasmaspheric hiss just inside the plasmapause boundary, with the inner edge of the outer radiation zone corresponding to the minimum plasmapause location. Recent observations have revealed unexpected radiation belt morphology, especially at ultrarelativistic kinetic energies (more than five megaelectronvolts). Here we analyse an extended data set that reveals an exceedingly sharp inner boundary for the ultrarelativistic electrons. Additional, concurrently measured data reveal that this barrier to inward electron radial transport does not arise because of a physical boundary within the Earth's intrinsic magnetic field, and that inward radial diffusion is unlikely to be inhibited by scattering by electromagnetic transmitter wave fields. Rather, we suggest that exceptionally slow natural inward radial diffusion combined with weak, but persistent, wave-particle pitch angle scattering deep inside the Earth's plasmasphere can combine to create an almost impenetrable barrier through which the most energetic Van Allen belt electrons cannot migrate.

  2. Mechanistic Insight into the Copper-Catalyzed Regiodivergent Silacarboxylation of Allenes with CO2.

    PubMed

    Yuan, Ruming; Hu, Rong; Fu, Gang

    2016-08-01

    DFT calculations were performed to investigate the detailed reaction mechanisms in the copper-catalyzed regiodivergent silacarboxylation of allenes. According to our calculations, the catalysis would bifurcate at the allene silylcupration step, followed by CO2 insertion, eventually leading to the carboxylated vinylsilane or allylsilane products. The gaps between the two silylcupration barriers were predicted to be -2.3, -0.4, and 2.2 kcal mol(-1) when using (rac)-Me-DuPhos, dcpe, and PCy3 (+H2 O) as the ligands, which nicely accounted for the experimental vinylsilane/allylsilane ratios of 93:7, 50:50, and 15:85, respectively. By means of transition-state-energy decomposition, we found that the energy penalty of catalyst deformation into its transition-state geometry was the key factor in determining the direction of the reaction. The switchable regioselectivity by using different P ligands could be ascribed to structural changes of the Cu-Si and Cu-P bonds during the silylcupration process. PMID:27319319

  3. An impenetrable barrier to ultrarelativistic electrons in the Van Allen radiation belts.

    PubMed

    Baker, D N; Jaynes, A N; Hoxie, V C; Thorne, R M; Foster, J C; Li, X; Fennell, J F; Wygant, J R; Kanekal, S G; Erickson, P J; Kurth, W; Li, W; Ma, Q; Schiller, Q; Blum, L; Malaspina, D M; Gerrard, A; Lanzerotti, L J

    2014-11-27

    Early observations indicated that the Earth's Van Allen radiation belts could be separated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons of moderate energy (less than about one megaelectronvolt) often populate both zones, with a deep 'slot' region largely devoid of particles between them. There is a region of dense cold plasma around the Earth known as the plasmasphere, the outer boundary of which is called the plasmapause. The two-belt radiation structure was explained as arising from strong electron interactions with plasmaspheric hiss just inside the plasmapause boundary, with the inner edge of the outer radiation zone corresponding to the minimum plasmapause location. Recent observations have revealed unexpected radiation belt morphology, especially at ultrarelativistic kinetic energies (more than five megaelectronvolts). Here we analyse an extended data set that reveals an exceedingly sharp inner boundary for the ultrarelativistic electrons. Additional, concurrently measured data reveal that this barrier to inward electron radial transport does not arise because of a physical boundary within the Earth's intrinsic magnetic field, and that inward radial diffusion is unlikely to be inhibited by scattering by electromagnetic transmitter wave fields. Rather, we suggest that exceptionally slow natural inward radial diffusion combined with weak, but persistent, wave-particle pitch angle scattering deep inside the Earth's plasmasphere can combine to create an almost impenetrable barrier through which the most energetic Van Allen belt electrons cannot migrate. PMID:25428500

  4. The relationship of the Allen Cognitive Level Test to cognitive abilities and psychopathology.

    PubMed

    David, S K; Riley, W T

    1990-06-01

    The cognitive factors measured by the Allen Cognitive Level Test (ACL) (Allen, 1982) as well as the test's relationship to level of psychopathology were examined through a retrospective study of 71 patients from a general hospital psychiatry unit. Pearson correlations, computed for the ACL score with the Shipley Institute of Living Scale (Shipley, 1940), a general measure of intellectual functioning, were significant. A strong correlation was found between the ACL and the Symbol-Digit Modalities Test (Smith, 1982), a measure of motor speed and concentration often used as a neurological screening instrument. This suggests the potential usefulness of the ACL to screen for cognitive dysfunctions associated with organicity. Contrary to hypothesis, there was no significant correlation between the ACL and measures of psychopathology such as the Beck Depression Inventory (Beck, Ward, Mendelson, Mock, & Erbaugh, 1961) and the Minnesota Multiphasic Personality Inventory (Hathaway & McKinley, 1940). The relationship of the ACL to other recognized measures of cognitive functioning increases its usefulness as a valid measure of day-to-day limitations in the functioning of psychiatric patients. Effective communication of the implications of these cognitive levels to a multidisciplinary treatment team is enhanced by knowledge of the relationship of the ACL to measures of cognitive functioning and psychopathology used by other disciplines.

  5. MRIVIEW: An interactive computational tool for investigation of brain structure and function

    SciTech Connect

    Ranken, D.; George, J.

    1993-12-31

    MRIVIEW is a software system which uses image processing and visualization to provide neuroscience researchers with an integrated environment for combining functional and anatomical information. Key features of the software include semi-automated segmentation of volumetric head data and an interactive coordinate reconciliation method which utilizes surface visualization. The current system is a precursor to a computational brain atlas. We describe features this atlas will incorporate, including methods under development for visualizing brain functional data obtained from several different research modalities.

  6. Using Frankenstein's creature paradigm to build a patient specific atlas.

    PubMed

    Commowick, Olivier; Warfield, Simon K; Malandain, Grégoire

    2009-01-01

    Conformal radiotherapy planning needs accurate delineations of the critical structures. Atlas-based segmentation has been shown to be very efficient to delineate brain structures. It would therefore be very interesting to develop an atlas for the head and neck region where 7% of the cancers arise. However, the construction of an atlas in this region is very difficult due to the high variability of the anatomies. This can generate segmentation errors and over-segmented structures in the atlas. To overcome this drawback, we present an alternative method to build a template locally adapted to the patient's anatomy. This is done first by selecting in a database the images that are the most similar to the patient on predefined regions of interest, using on a distance between transformations. The first major contribution is that we do not compute every patient-to-image registration to find the most similar image, but only the registration of the patient towards an average image. This method is therefore computationally very efficient. The second major contribution is a novel method to use the selected images and the predefined regions to build a "Frankenstein's creature" for segmentation. We present a qualitative and quantitative comparison between the proposed method and a classical atlas-based segmentation method. This evaluation is performed on a subset of 58 patients among a database of 105 head and neck CT images and shows a great improvement of the specificity of the results. PMID:20426208

  7. ATLAS Metadata Task Force

    SciTech Connect

    ATLAS Collaboration; Costanzo, D.; Cranshaw, J.; Gadomski, S.; Jezequel, S.; Klimentov, A.; Lehmann Miotto, G.; Malon, D.; Mornacchi, G.; Nemethy, P.; Pauly, T.; von der Schmitt, H.; Barberis, D.; Gianotti, F.; Hinchliffe, I.; Mapelli, L.; Quarrie, D.; Stapnes, S.

    2007-04-04

    This document provides an overview of the metadata, which are needed to characterizeATLAS event data at different levels (a complete run, data streams within a run, luminosity blocks within a run, individual events).

  8. Diabetes Interactive Atlas

    PubMed Central

    Burrows, Nilka R.; Geiss, Linda S.

    2014-01-01

    The Diabetes Interactive Atlas is a recently released Web-based collection of maps that allows users to view geographic patterns and examine trends in diabetes and its risk factors over time across the United States and within states. The atlas provides maps, tables, graphs, and motion charts that depict national, state, and county data. Large amounts of data can be viewed in various ways simultaneously. In this article, we describe the design and technical issues for developing the atlas and provide an overview of the atlas’ maps and graphs. The Diabetes Interactive Atlas improves visualization of geographic patterns, highlights observation of trends, and demonstrates the concomitant geographic and temporal growth of diabetes and obesity. PMID:24503340

  9. From the IGY to the IHY: A Changing View of the Van Allen Radiation Belts

    NASA Astrophysics Data System (ADS)

    Hudson, M. K.

    2006-12-01

    Discovery of the Van Allen radiation belts by instrumentation flown on Explorer 1 in 1958 was the first major discovery of the Space Age. A view of the belts as static inner and outer zones of energetic particles with different sources, a double-doughnut encircling the Earth, became iconic to the point that their dynamic behavior and solar connection receded from public awareness and apparent scientific import. Then the Cycle 23 maximum in solar activity arrived in 1989-1991, the first approaching the activity level of the International Geophysical Year of 1957-58, when the Van Allen belts were first discovered. Delay in launch of the NASA-Air Force Combined Radiation Release and Effects Satellite, following the Challenger accident in 1986, led to having the right instruments in the right orbit at the right time to detect prompt injection of outer belt electrons and solar energetic protons into the `slot region' between the inner and outer belts, forming new trapped populations which lasted for years in an otherwise benign location. This event in March 1991, along with the great geomagnetic storm of March 1989, and our increased dependence on space technology since the early Explorer days, led to a resurgence of interest in the Van Allen radiation belts and understanding of their connectivity to the Sun. Additional instrumentation from NASA's International Solar Terrestrial Physics Program, the Solar Anomalous and Magnetospheric Particle Explorer (SAMPEX) and IMAGE spacecraft from the Explorer program, NOAA and DOD spacecraft, and improved worldwide linkages of groundbased measurements have contributed much since 1991 to our understanding of the dynamic characteristics of the Van Allen belts. Further, the presence of continuous solar wind measurements beginning with the launch of WIND in 1994, and SOHO images of Coronal Mass Ejections and coronal hole sources of high speed solar wind flow have filled in the connection with solar activity qualitatively anticipated

  10. Allylic and Allenic Halide Synthesis via NbCl5- and NbBr5-Mediated Alkoxide Rearrangements

    PubMed Central

    Ravikumar, P. C.; Yao, Lihua; Fleming, Fraser F.

    2009-01-01

    Addition of NbCl5, or NbBr5, to a series of magnesium, lithium, or potassium allylic or propargylic alkoxides directly provides allylic or allenic halides. Halogenation formally occurs through a metalla-halo-[3,3] rearrangement although concerted, ionic, and direct displacement mechanisms appear to operate competitively. Transposition of the olefin is equally effective for allylic alkoxides prepared by nucleophilic addition, deprotonation, or reduction. Experimentally, the niobium pentahalide halogenations are rapid, afford essentially pure E-allylic or allenic halides after extraction, and are applicable to a range of aliphatic and aromatic alcohols, aldehydes, and ketones. PMID:19739606

  11. Allylic and allenic halide synthesis via NbCl(5)- and NbBr(5)-mediated alkoxide rearrangements.

    PubMed

    Ravikumar, P C; Yao, Lihua; Fleming, Fraser F

    2009-10-01

    Addition of NbCl(5) or NbBr(5) to a series of magnesium, lithium, or potassium allylic or propargylic alkoxides directly provides allylic or allenic halides. Halogenation formally occurs through a metalla-halo-[3,3] rearrangement, although concerted, ionic, and direct displacement mechanisms appear to operate competitively. Transposition of the olefin is equally effective for allylic alkoxides prepared by nucleophilic addition, deprotonation, or reduction. Experimentally, the niobium pentahalide halogenations are rapid, afford essentially pure (E)-allylic or -allenic halides after extraction, and are applicable to a range of aliphatic and aromatic alcohols, aldehydes, and ketones. PMID:19739606

  12. On the generation of large amplitude spiky solitons by ultralow frequency earthquake emission in the Van Allen radiation belt

    SciTech Connect

    Mofiz, U. A.

    2006-08-15

    The parametric coupling between earthquake emitted circularly polarized electromagnetic radiation and ponderomotively driven ion-acoustic perturbations in the Van Allen radiation belt is considered. A cubic nonlinear Schroedinger equation for the modulated radiation envelope is derived, and then solved analytically. For ultralow frequency earthquake emissions large amplitude spiky supersonic bright solitons or subsonic dark solitons are found to be generated in the Van Allen radiation belt, detection of which can be a tool for the prediction of a massive earthquake may be followed later.

  13. Use of a New Spirophosphine to Achieve Catalytic Enantioselective [4+1] Annulations of Amines with Allenes to Generate Dihydropyrroles

    PubMed Central

    Kramer, Søren; Fu, Gregory C.

    2015-01-01

    Due in part to the common occurrence of five-membered nitrogen heterocycles in bioactive molecules, the discovery of methods for the enantioselective synthesis of such structures is a useful endeavor. Building on a single example by Tong of a phosphine-catalyzed [4+1] annulation of an amine with an allene that furnished an achiral dihydropyrrole in 22% yield, we have developed, with the aid of a new chiral spirophosphine catalyst, a method with increased utility, specifically, improved yield, enhanced scope (the use of γ-substituted allenes), and good ee. The enantioenriched dihydropyrrole products can be transformed into other interesting families of compounds with very good stereoselectivity. PMID:25780940

  14. Construction of 4D high-definition cortical surface atlases of infants: Methods and applications.

    PubMed

    Li, Gang; Wang, Li; Shi, Feng; Gilmore, John H; Lin, Weili; Shen, Dinggang

    2015-10-01

    In neuroimaging, cortical surface atlases play a fundamental role for spatial normalization, analysis, visualization, and comparison of results across individuals and different studies. However, existing cortical surface atlases created for adults are not suitable for infant brains during the first two postnatal years, which is the most dynamic period of postnatal structural and functional development of the highly-folded cerebral cortex. Therefore, spatiotemporal cortical surface atlases for infant brains are highly desired yet still lacking for accurate mapping of early dynamic brain development. To bridge this significant gap, leveraging our infant-dedicated computational pipeline for cortical surface-based analysis and the unique longitudinal infant MRI dataset acquired in our research center, in this paper, we construct the first spatiotemporal (4D) high-definition cortical surface atlases for the dynamic developing infant cortical structures at seven time points, including 1, 3, 6, 9, 12, 18, and 24 months of age, based on 202 serial MRI scans from 35 healthy infants. For this purpose, we develop a novel method to ensure the longitudinal consistency and unbiasedness to any specific subject and age in our 4D infant cortical surface atlases. Specifically, we first compute the within-subject mean cortical folding by unbiased groupwise registration of longitudinal cortical surfaces of each infant. Then we establish longitudinally-consistent and unbiased inter-subject cortical correspondences by groupwise registration of the geometric features of within-subject mean cortical folding across all infants. Our 4D surface atlases capture both longitudinally-consistent dynamic mean shape changes and the individual variability of cortical folding during early brain development. Experimental results on two independent infant MRI datasets show that using our 4D infant cortical surface atlases as templates leads to significantly improved accuracy for spatial normalization

  15. Crystallization and Preliminary X-ray Analysis of Allene Oxide Synthase, Cytochrome P450 CYP74A2, from Parthenium argentatum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oxylipins are oxygenated derivatives of fatty acids and pivotal signaling molecules in plants and animals. Allene oxide synthase (AOS) is a key cytochrome P450 CYP74 enzyme involved in the biosynthesis of plant oxylipin jasmonates to convert 13(S)-hydroperoxide to allene oxide. Guayule (Parthenium a...

  16. Complete transfer of chirality in an intramolecular, thermal [2 + 2] cycloaddition of allene-ynes to form non-racemic spirooxindoles.

    PubMed

    Brummond, Kay M; Osbourn, Joshua M

    2011-01-01

    A thermal [2 + 2] cycloaddition reaction of allene-ynes has been used to transform chiral non-racemic allenyl oxindoles into chiral non-racemic spirooxindoles containing an alkylidene cyclobutene moiety. The enantiomeric excesses were determined by chiral lanthanide shift NMR analysis and the transfer of chiral information from the allene to the spirooxindole was found to be greater than 95%.

  17. ATLAS@AWS

    NASA Astrophysics Data System (ADS)

    Gehrcke, Jan-Philip; Kluth, Stefan; Stonjek, Stefan

    2010-04-01

    We show how the ATLAS offline software is ported on the Amazon Elastic Compute Cloud (EC2). We prepare an Amazon Machine Image (AMI) on the basis of the standard ATLAS platform Scientific Linux 4 (SL4). Then an instance of the SLC4 AMI is started on EC2 and we install and validate a recent release of the ATLAS offline software distribution kit. The installed software is archived as an image on the Amazon Simple Storage Service (S3) and can be quickly retrieved and connected to new SL4 AMI instances using the Amazon Elastic Block Store (EBS). ATLAS jobs can then configure against the release kit using the ATLAS configuration management tool (cmt) in the standard way. The output of jobs is exported to S3 before the SL4 AMI is terminated. Job status information is transferred to the Amazon SimpleDB service. The whole process of launching instances of our AMI, starting, monitoring and stopping jobs and retrieving job output from S3 is controlled from a client machine using python scripts implementing the Amazon EC2/S3 API via the boto library working together with small scripts embedded in the SL4 AMI. We report our experience with setting up and operating the system using standard ATLAS job transforms.

  18. Spatially adapted augmentation of age-specific atlas-based segmentation using patch-based priors

    NASA Astrophysics Data System (ADS)

    Liu, Mengyuan; Seshamani, Sharmishtaa; Harrylock, Lisa; Kitsch, Averi; Miller, Steven; Chau, Van; Poskitt, Kenneth; Rousseau, Francois; Studholme, Colin

    2014-03-01

    One of the most common approaches to MRI brain tissue segmentation is to employ an atlas prior to initialize an Expectation- Maximization (EM) image labeling scheme using a statistical model of MRI intensities. This prior is commonly derived from a set of manually segmented training data from the population of interest. However, in cases where subject anatomy varies significantly from the prior anatomical average model (for example in the case where extreme developmental abnormalities or brain injuries occur), the prior tissue map does not provide adequate information about the observed MRI intensities to ensure the EM algorithm converges to an anatomically accurate labeling of the MRI. In this paper, we present a novel approach for automatic segmentation of such cases. This approach augments the atlas-based EM segmentation by exploring methods to build a hybrid tissue segmentation scheme that seeks to learn where an atlas prior fails (due to inadequate representation of anatomical variation in the statistical atlas) and utilize an alternative prior derived from a patch driven search of the atlas data. We describe a framework for incorporating this patch-based augmentation of EM (PBAEM) into a 4D age-specific atlas-based segmentation of developing brain anatomy. The proposed approach was evaluated on a set of MRI brain scans of premature neonates with ages ranging from 27.29 to 46.43 gestational weeks (GWs). Results indicated superior performance compared to the conventional atlas-based segmentation method, providing improved segmentation accuracy for gray matter, white matter, ventricles and sulcal CSF regions.

  19. Low-Rank Atlas Image Analyses in the Presence of Pathologies.

    PubMed

    Liu, Xiaoxiao; Niethammer, Marc; Kwitt, Roland; Singh, Nikhil; McCormick, Matt; Aylward, Stephen

    2015-12-01

    We present a common framework, for registering images to an atlas and for forming an unbiased atlas, that tolerates the presence of pathologies such as tumors and traumatic brain injury lesions. This common framework is particularly useful when a sufficient number of protocol-matched scans from healthy subjects cannot be easily acquired for atlas formation and when the pathologies in a patient cause large appearance changes. Our framework combines a low-rank-plus-sparse image decomposition technique with an iterative, diffeomorphic, group-wise image registration method. At each iteration of image registration, the decomposition technique estimates a "healthy" version of each image as its low-rank component and estimates the pathologies in each image as its sparse component. The healthy version of each image is used for the next iteration of image registration. The low-rank and sparse estimates are refined as the image registrations iteratively improve. For unbiased atlas formation, at each iteration, the average of the low-rank images from the patients is used as the atlas image for the next iteration, until convergence. Since each iteration's atlas is comprised of low-rank components, it provides a population-consistent, pathology-free appearance. Evaluations of the proposed methodology are presented using synthetic data as well as simulated and clinical tumor MRI images from the brain tumor segmentation (BRATS) challenge from MICCAI 2012.

  20. Comparison of species-resolved energy spectra from ACE EPAM and Van Allen Probes RBSPICE

    NASA Astrophysics Data System (ADS)

    Patterson, J.; Manweiler, J. W.; Armstrong, T. P.; Lanzerotti, L. J.; Gerrard, A. J.; Gkioulidou, M.

    2013-12-01

    We present a comparison between energy spectra measured by the Advanced Composition Explorer (ACE) Electron Proton Alpha Monitor (EPAM) instrument and the Van Allen Probe Ion Composition Experiment (RBSPICE) for two significant and distinct events in early 2013. The first is an impulsive solar particle event on March 17th. While intense, this event presented no significant surprises in terms of its composition or anisotropy characteristics, thus providing a good baseline for response of the trapped radiation belts as observed by the Van Allen Probes. The second solar event occurred late May 22nd and early May 23rd. This event has a much greater concentration of medium and heavy ions than the St. Patrick's Day event, as well as having very peculiar energy spectra with evidence of two distinct populations. During the St. Patrick's Day Event, the energy spectra for helium, carbon, oxygen, neon, silicon, and iron all show the same spectral power law slope -3.1. The event shows strong anisotropy with intensities differing by a factor of four for both protons and Z>1 ions. The late May event also has strong anisotropy, and in the same directions as the St. Patrick's Day Event, but with very different composition and energy spectra. The spectra are much harder with power law spectral slopes of -0.5. Additionally, there is a significant spectral bump at 3 MeV/nuc for helium that is not present in the spectra of the heavier ions. The intensities of the heavier ions, however, show an increase that is an order of magnitude greater than the increase seen for helium. The March 17 RBSPICE observations show multiple injection events lasting for less than an hour each during the Van Allen Probes B apogees. These injections are seen in protons as well as Helium and only somewhat observed in Oxygen. Spectral slopes for the observations range from approximately -5 during quiet times to double peaked events with a spectral slope of approximately -2 at the beginning of the injection

  1. Atlas-based segmentation of brainstem regions in neuromelanin-sensitive magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Puigvert, Marc; Castellanos, Gabriel; Uranga, Javier; Abad, Ricardo; Fernández-Seara, María. A.; Pastor, Pau; Pastor, María. A.; Muñoz-Barrutia, Arrate; Ortiz de Solórzano, Carlos

    2015-03-01

    We present a method for the automatic delineation of two neuromelanin rich brainstem structures -substantia nigra pars compacta (SN) and locus coeruleus (LC)- in neuromelanin sensitive magnetic resonance images of the brain. The segmentation method uses a dynamic multi-image reference atlas and a pre-registration atlas selection strategy. To create the atlas, a pool of 35 images of healthy subjects was pair-wise pre-registered and clustered in groups using an affinity propagation approach. Each group of the atlas is represented by a single exemplar image. Each new target image to be segmented is registered to the exemplars of each cluster. Then all the images of the highest performing clusters are enrolled into the final atlas, and the results of the registration with the target image are propagated using a majority voting approach. All registration processes used combined one two-stage affine and one elastic B-spline algorithm, to account for global positioning, region selection and local anatomic differences. In this paper, we present the algorithm, with emphasis in the atlas selection method and the registration scheme. We evaluate the performance of the atlas selection strategy using 35 healthy subjects and 5 Parkinson's disease patients. Then, we quantified the volume and contrast ratio of neuromelanin signal of these structures in 47 normal subjects and 40 Parkinson's disease patients to confirm that this method can detect neuromelanin-containing neurons loss in Parkinson's disease patients and could eventually be used for the early detection of SN and LC damage.

  2. Spatial normalization of brain images and beyond.

    PubMed

    Mangin, J-F; Lebenberg, J; Lefranc, S; Labra, N; Auzias, G; Labit, M; Guevara, M; Mohlberg, H; Roca, P; Guevara, P; Dubois, J; Leroy, F; Dehaene-Lambertz, G; Cachia, A; Dickscheid, T; Coulon, O; Poupon, C; Rivière, D; Amunts, K; Sun, Z Y

    2016-10-01

    The deformable atlas paradigm has been at the core of computational anatomy during the last two decades. Spatial normalization is the variant endowing the atlas with a coordinate system used for voxel-based aggregation of images across subjects and studies. This framework has largely contributed to the success of brain mapping. Brain spatial normalization, however, is still ill-posed because of the complexity of the human brain architecture and the lack of architectural landmarks in standard morphological MRI. Multi-atlas strategies have been developed during the last decade to overcome some difficulties in the context of segmentation. A new generation of registration algorithms embedding architectural features inferred for instance from diffusion or functional MRI is on the verge to improve the architectural value of spatial normalization. A better understanding of the architectural meaning of the cortical folding pattern will lead to use some sulci as complementary constraints. Improving the architectural compliance of spatial normalization may impose to relax the diffeomorphic constraint usually underlying atlas warping. A two-level strategy could be designed: in each region, a dictionary of templates of incompatible folding patterns would be collected and matched in a way or another using rare architectural information, while individual subjects would be aligned using diffeomorphisms to the closest template. Manifold learning could help to aggregate subjects according to their morphology. Connectivity-based strategies could emerge as an alternative to deformation-based alignment leading to match the connectomes of the subjects rather than images.

  3. Spatial normalization of brain images and beyond.

    PubMed

    Mangin, J-F; Lebenberg, J; Lefranc, S; Labra, N; Auzias, G; Labit, M; Guevara, M; Mohlberg, H; Roca, P; Guevara, P; Dubois, J; Leroy, F; Dehaene-Lambertz, G; Cachia, A; Dickscheid, T; Coulon, O; Poupon, C; Rivière, D; Amunts, K; Sun, Z Y

    2016-10-01

    The deformable atlas paradigm has been at the core of computational anatomy during the last two decades. Spatial normalization is the variant endowing the atlas with a coordinate system used for voxel-based aggregation of images across subjects and studies. This framework has largely contributed to the success of brain mapping. Brain spatial normalization, however, is still ill-posed because of the complexity of the human brain architecture and the lack of architectural landmarks in standard morphological MRI. Multi-atlas strategies have been developed during the last decade to overcome some difficulties in the context of segmentation. A new generation of registration algorithms embedding architectural features inferred for instance from diffusion or functional MRI is on the verge to improve the architectural value of spatial normalization. A better understanding of the architectural meaning of the cortical folding pattern will lead to use some sulci as complementary constraints. Improving the architectural compliance of spatial normalization may impose to relax the diffeomorphic constraint usually underlying atlas warping. A two-level strategy could be designed: in each region, a dictionary of templates of incompatible folding patterns would be collected and matched in a way or another using rare architectural information, while individual subjects would be aligned using diffeomorphisms to the closest template. Manifold learning could help to aggregate subjects according to their morphology. Connectivity-based strategies could emerge as an alternative to deformation-based alignment leading to match the connectomes of the subjects rather than images. PMID:27344104

  4. Dialogic Considerations of Confrontation as a Counseling Activity: An Examination of Allen Ivey's Use of Confronting as a Microskill

    ERIC Educational Resources Information Center

    Strong, Tom; Zeman, Don

    2010-01-01

    The authors examine confrontation as a communication skill practiced and described by counselor educator Allen Ivey. Seeing confrontation as a dialogic activity completed interactionally, they use conversation analysis to examine 2 passages where Ivey used confrontation in his teaching tapes. Their microanalyses highlight some important and…

  5. Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk from Leo Holberg and Allen Mills

    ScienceCinema

    Holberg, Leo; Mills, Allen [NIST

    2016-07-12

    Leo Holberg and Allen Mills present a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

  6. Expression of concern: A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones.

    PubMed

    Kelly, Richard

    2015-12-21

    Expression of concern for 'A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones' by Adán B. González-Pérez et al., Org. Biomol. Chem., 2014, 12, 7694-7701. PMID:26575412

  7. Van Allen Probes, NOAA, and Ground Observations of an Intense Pc 1 Wave Event Extending 12 Hours in MLT

    NASA Astrophysics Data System (ADS)

    Engebretson, M. J.; Posch, J. L.; Wygant, J. R.; Kletzing, C.; Lessard, M.; Horne, R. B.; Reeves, G. D.; Gkioulidou, M.; Fennell, J.; Oksavik, K.; Raita, T.

    2014-12-01

    On February 23, 2014 a Pc 1 wave event extending 8 hours in UT and 12 hours in MLT was observed at Halley, Antarctica and Ivalo, Finland in the dawn sector, and by both Van Allen Probes spacecraft from late morning through local noon. The wave activity was stimulated by a gradual 4-hour rise and subsequent sharp increases in solar wind pressure. Intense hydrogen band, linearly polarized Pc 1 wave activity (up to 25 nT p-p) with very similar time variations also appeared for over 4 hours at both Van Allen Probes, located ~8 and ~9 hours east of Halley. Waves appeared when these spacecraft were outside the plasmapause, with densities ~5-20 cm-3. Ten passes of NOAA-POES and METOP satellites near the northern hemisphere footpoint of the Van Allen Probes (over Siberia) show the presence of 30-80 keV subauroral proton precipitation. This is the longest-duration and most intense Pc1 event we have yet observed with the Van Allen Probes. The combination of its duration, intensity, and large local time extent (from before 02 to nearly 14 hours MLT) suggests that it might have a significant effect on the ring current, and possibly even electrons in the outer radiation belt.

  8. Dehydrogenative [2 + 2 + 2] Cycloaddition of Cyano-yne-allene Substrates: Convenient Access to 2,6-Naphthyridine Scaffolds.

    PubMed

    Haraburda, Ewelina; Lledó, Agustí; Roglans, Anna; Pla-Quintana, Anna

    2015-06-19

    A rhodium-catalyzed [2 + 2 + 2] cycloaddition of cyano-yne-allene scaffolds followed by a dehydrogenative process enabling the direct synthesis of unsaturated pyridine-containing compounds that can be conveniently converted to 2,6-naphthyridine derivatives is reported.

  9. Remarkable new results for high-energy protons and electrons in the inner Van Allen belt regions

    NASA Astrophysics Data System (ADS)

    Baker, Daniel N.

    2016-04-01

    Early observations indicated that the Earth's Van Allen radiation belts could be separated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons of moderate energy (less than about one megaelectronvolt) often populate both zones, with a deep 'slot' region largely devoid of particles between them. The two-belt radiation structure was explained as arising from strong electron interactions with plasmaspheric hiss just inside the plasmapause boundary with the inner edge of the outer radiation zone corresponding to the minimum plasmapause location.. Recent Van Allen Probes observations have revealed an unexpected radiation belt morphology, especially at ultrarelativistic kinetic energies (more than several megaelectronvolts). The data show an exceedingly sharp inner boundary for the ultrarelativistic electrons right at L=2.8. Additional, concurrently measured data reveal that this barrier to inward electron radial transport is likely due to scattering by powerful human electromagnetic transmitter (VLF) wave fields. We show that weak, but persistent, wave-particle pitch angle scattering deep inside the Earth's plasmasphere due to manmade signals can act to create an almost impenetrable barrier through which the most energetic Van Allen belt electrons cannot migrate. Inside of this distance, the Van Allen Probes data show that high energy (20 -100 MeV) protons have a double belt structure with a stable peak of flux at L~1.5 and a much more variable belt peaking at L~2.3.

  10. Choctaw Leadership in Oklahoma: The Allen Wright Family and Education in the Nineteenth and Early Twentieth Centuries

    ERIC Educational Resources Information Center

    Noley, Grayson; Smith, Joan K.; Vaughn, Courtney; Cesar, Dana

    2009-01-01

    Against the backdrop of internal colonialism, this article examines the educational and social lives of Allen Wright and his children to better understand how this Choctaw family successfully navigated the pressures of dual cultures by: (1) providing the socio-political context of the indigenous culture prior to Wright's birth; (2) chronicling and…

  11. Wave-driven butterfly distribution of Van Allen belt relativistic electrons

    PubMed Central

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D. N.; Spence, H. E.; Funsten, H. O.; Blake, J. B.

    2015-01-01

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day–night asymmetry in Earth's magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. Simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. The current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons. PMID:26436770

  12. Van Allen Probes observations of oxygen cyclotron harmonic waves in the inner magnetosphere

    NASA Astrophysics Data System (ADS)

    Usanova, M. E.; Malaspina, D. M.; Jaynes, A. N.; Bruder, R. J.; Mann, I. R.; Wygant, J. R.; Ergun, R. E.

    2016-09-01

    Waves with frequencies in the vicinity of the oxygen cyclotron frequency and its harmonics have been regularly observed on the Van Allen Probes satellites during geomagnetic storms. We focus on properties of these waves and present events from the main phase of two storms on 1 November 2012 and 17 March 2013 and associated dropouts of a few MeV electron fluxes. They are electromagnetic, in the frequency range ~0.5 to several Hz, and amplitude ~0.1 to a few nT in magnetic and ~0.1 to a few mV/m in electric field, with both the wave velocity and the Poynting vector directed almost parallel to the background magnetic field. These properties are very similar to those of electromagnetic ion cyclotron waves, which are believed to contribute to loss of ring current ions and radiation belt electrons and therefore can be also important for inner magnetosphere dynamics.

  13. Fractional Cahn-Hilliard, Allen-Cahn and porous medium equations

    NASA Astrophysics Data System (ADS)

    Akagi, Goro; Schimperna, Giulio; Segatti, Antonio

    2016-09-01

    We introduce a fractional variant of the Cahn-Hilliard equation settled in a bounded domain Ω ⊂RN and complemented with homogeneous Dirichlet boundary conditions of solid type (i.e., imposed in the whole of RN ∖ Ω). After setting a proper functional framework, we prove existence and uniqueness of weak solutions to the related initial-boundary value problem. Then, we investigate some significant singular limits obtained as the order of either of the fractional Laplacians appearing in the equation is let tend to 0. In particular, we can rigorously prove that the fractional Allen-Cahn, fractional porous medium, and fractional fast-diffusion equations can be obtained in the limit. Finally, in the last part of the paper, we discuss existence and qualitative properties of stationary solutions of our problem and of its singular limits.

  14. Real-time beamforming using high-speed FPGAs at the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Barott, William C.; Milgrome, Oren; Wright, Melvyn; MacMahon, David; Kilsdonk, Tom; Backus, Peter; Dexter, Matt

    2011-02-01

    The Allen Telescope Array (ATA) at the Hat Creek Radio Observatory (HCRO) is a wide-field panchromatic radio telescope currently consisting of 42 offset-Gregorian antennas each with a 6 m aperture, with plans to expand the array to 350 antennas. Through unique back-end hardware, the ATA performs real-time wideband beamforming with independent subarray capabilities and customizable beam shaping. The beamformers enable science observations requiring the full gain of the array, time domain (nonintegrated) output, and interference excision or orthogonal beamsets. In this paper we report on the design of this beamformer, including architecture and experimental results. Furthermore, we address some practical considerations in large-N wideband beamformers implemented on field programmable gate array platforms, including device utilization, methods of calibration and control, and interchip synchronization.

  15. Five Years of SETI with the Allen Telescope Array: Lessons Learned

    NASA Astrophysics Data System (ADS)

    Harp, Gerald

    2016-01-01

    We discuss recent observations at the Allen Telescope Array (ATA) supporting a wide ranging Search for Extraterrestrial Intelligence (SETI). The ATA supports observations over the frequency range 1-10 GHz with three simultaneous phased array beams used in an anticoincidence detector for false positive rejection. Here we summarize observational results over the years 2011-2015 covering multiple campaigns of exoplanet stars, the galactic plane, infrared excess targets, etc. Approximately 2 x 108 signals were identified and classified over more than 5000 hours of observation. From these results we consider various approaches to the rapid identification of human generated interference in the process of the search for a signal with origins outside the radius of the Moon's orbit. We conclude that the multi-beam technique is superb tool for answering the very difficult question of the direction of origin of signals. Data-based simulations of future instruments with more than 3 beams are compared.

  16. Van Allen Probes Multipoint Measurements of the Spatial and Coherence Scales of EMIC Waves

    NASA Astrophysics Data System (ADS)

    Blum, L. W.; Bonnell, J. W.; Agapitov, O. V.; Bortnik, J.

    2015-12-01

    Electromagnetic ion cyclotron (EMIC) waves are able to resonate with MeV electrons and cause precipitation loss of radiation belt electrons. EMIC waves can provide a strong source of electron pitch angle diffusion, but the waves are often quite localized - thus the spatial extents of these waves can have a large effect on their overall scattering efficiency. Using measurements from the Van Allen Probes, we characterize the spatial extents of EMIC wave active regions, and how these depend on local time, radial distance, and driver. As the separation between the spacecraft along the orbital track varies in time, with one spacecraft lapping the other every ~70 days, we can determine the correlation between EMIC wave measurements at varying spacecraft separations. During individual events at close approaches (Jan 17 2013, for example - see attached figure), analysis of the detailed wave properties and coherence is performed. These studies provide important information on parameters relevant for determining resonance of EMIC waves with radiation belt electrons.

  17. Penetration of magnetosonic waves into the plasmasphere observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Xiao, F.; Zhou, Q.; He, Y.; Yang, C.; Liu, S.; Baker, D. N.; Spence, H. E.; Reeves, G. D.; Funsten, H. O.; Blake, J. B.

    2015-12-01

    During the small storm on 14-15 April 2014, Van Allen Probe A measured a continuously distinct proton ring distribution and enhanced magnetosonic (MS) waves along their orbit outside the plasmapause. Inside the plasmasphere, strong MS waves were still present but the distinct proton ring distribution was falling steeply with distance. We adopt a sum of subtracted bi-Maxwellian components to model the observed proton ring distribution and simulate the wave trajectory and growth. MS waves at first propagate towards lower L-shells outside the plasmasphere, with rapidly increasing path gains related to the continuous proton ring distribution. Then they gradually cross the plasmapause into the deep plasmasphere, with almost unchanged path gains due to the falling proton ring distribution and higher ambient density. These results present the first report on how MS waves penetrate into the plasmasphere with aid of the continuous proton ring distributions during weak geomagnetic activities.

  18. Crossed molecular beam study of the reaction O([sup 3][ital P])+allene

    SciTech Connect

    Schmoltner, A.M.; Huang, S.Y.; Brudzynski, R.J.; Chu, P.M.; Lee, Y.T. )

    1993-08-01

    The reaction between ground state ([sup 3][ital P]) oxygen atoms and allene was studied under single collision conditions using the crossed molecular beams method. Product angular distributions and the translational energy distribution were determined for each channel. Two major reaction channels could be identified unambiguously: the formation of carbon monoxide and ethylene following oxygen atom attack on the central carbon atom, and the formation of allenyloxy (formyl--vinyl) radical and hydrogen atom following oxygen atom attack on the terminal carbon atom. In addition, at least one other reaction channel, which could be identified as the production of vinyl and formyl radicals, occurs. This channel involves the decomposition of acrolein which is formed by the addition of oxygen to the terminal carbon atom, followed by 1,2-hydrogen migration.

  19. Convection Electric Field Observations by THEMIS and the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Califf, S.; Li, X.; Bonnell, J. W.; Wygant, J. R.; Malaspina, D.; Hartinger, M.; Thaller, S. A.

    2013-12-01

    We present direct electric field measurements made by THEMIS and the Van Allen Probes in the inner magnetosphere, focusing on the large-scale, near-DC convection electric field. The convection electric field drives plasma Earthward from the tail into the inner magnetosphere, playing a critical role in forming the ring current. Although it is normally shielded deep inside the magnetosphere, during storm times this large-scale electric field can penetrate to low L values (L < 3), eroding the plasmasphere and also providing a mechanism for ~100 keV electron injection into the slot region and inner radiation belt. The relationship of the convection electric field with the plasmasphere is also important for understanding the dynamic outer radiation belt, as the plasmapause boundary has been strongly correlated with the dynamic variation of the outer radiation belt electrons.

  20. Wave-driven butterfly distribution of Van Allen belt relativistic electrons

    SciTech Connect

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D. N.; Spence, H. E.; Funsten, H. O.; Blake, J. B.

    2015-10-05

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day–night asymmetry in Earth’s magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. In conclusion, simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. Finally, the current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons.

  1. Wave-driven butterfly distribution of Van Allen belt relativistic electrons.

    PubMed

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D N; Spence, H E; Funsten, H O; Blake, J B

    2015-01-01

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day-night asymmetry in Earth's magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. Simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. The current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons.

  2. EMIC wave spatial and coherence scales as determined from multipoint Van Allen Probe measurements

    NASA Astrophysics Data System (ADS)

    Blum, L. W.; Agapitov, O.; Bonnell, J. W.; Kletzing, C.; Wygant, J.

    2016-05-01

    Electromagnetic ion cyclotron (EMIC) waves can provide a strong source of energetic electron pitch angle scattering. These waves are often quite localized, thus their spatial extent can have a large effect on their overall scattering efficiency. Using measurements from the dual Van Allen Probes, we examine four EMIC wave events observed simultaneously on the two probes at varying spacecraft separations. Correlation of both the wave amplitude and phase observed at both spacecraft is examined to estimate the active region and coherence scales of the waves. We find well-correlated wave amplitude and amplitude modulation across distances spanning hundreds to thousands of kilometers. Phase coherence persisting 30-60 s is observable during close conjunction events but is lost as spacecraft separations exceed ~1 Earth Radii.

  3. Inner zone electron radial diffusion coefficients - An update with Van Allen Probes MagEIS data

    NASA Astrophysics Data System (ADS)

    O'Brien, Paul; Fennell, Joseph; Guild, Timothy; Mazur, Joseph; Claudepierre, Seth; Clemmons, James; Turner, Drew; Blake, Bernard; Roeder, James

    2016-07-01

    Using MagEIS data from NASA's recent Van Allen Probes mission, we estimate the quiet-time radial diffusion coefficients for electrons in the inner radiation belt and slot, for energies up to ~700 keV. We provide observational evidence that energy diffusion is negligible. The main dynamic processes, then, are radial diffusion and elastic pitch angle scattering. We use a coordinate system in which these two modes of diffusion are separable. Then we integrate over pitch angle to obtain a field line content whose dynamics consist of radial diffusion and loss to the atmosphere. We estimate the loss timescale from periods of exponential decay in the time series. We then estimate the radial diffusion coefficient from the temporal and radial variation of the field line content. We show that our diffusion coefficients agree well with previously determined values. Our coefficients are consistent with diffusion by electrostatic impulses, whereas outer zone radial diffusion is thought to be dominated by electromagnetic fluctuations.

  4. "Her mouth is medicine": Beth Brant and Paula Gunn Allen's decolonizing queer erotics.

    PubMed

    Burford, Arianne

    2013-01-01

    This article asserts the need to recognize the complexity of the theoretical work of more lesbian Native American writers, focusing specifically Beth Brant (Bay of Quinte Mohawk) and Paula Gunn Allen (Laguna Pueblo). Their poetry and short stories provide a theoretically nuanced analysis of how heteronormativity is intertwined in and dependent on colonialism, and thus a methodology for Queer Theory that requires an understanding of it in relation to colonialism. They reject heteronormative Pocahontas fantasies about Native women, offering a lesbian-based tactic for decolonization through the expression of erotic desire. This article demonstrates the endless possibilities for fierce queer resistance, revolutionary change, and healing from the trauma of genocide and the accompanying colonialist heteropatriarchal disciplining of Native women's bodies.

  5. Computational and experimental investigations of the formal dyotropic rearrangements of Himbert arene/allene cycloadducts.

    PubMed

    Pham, Hung V; Karns, Alexander S; Vanderwal, Christopher D; Houk, K N

    2015-06-01

    The fascinating intramolecular arene/allene cycloaddition discovered by Himbert affords dearomatized, polycyclic intermediates with sufficient strain energy to drive rearrangement processes of the newly formed ring system. We disclose a detailed examination of a thermally induced stepwise dyotropic skeletal rearrangement of these cycloadducts, a reaction also first described by Himbert. We offer computational evidence for a two-stage mechanism for this formal dyotropic rearrangement and provide rationalizations for the significant substitution-dependent rate differences observed in experiments. These investigations led to the development of a Lewis-acid-catalyzed rearrangement of precursors that were unreactive under simple thermal instigation. The isolation of the product of an "interrupted" rearrangement under Lewis acidic conditions provides further support for the proposed stepwise mechanism. Computational results also matched experiments in terms of regiochemical preferences in unsymmetrical rearrangement precursors and explained why lactam O-, S-, and C-heterologues do not easily undergo this rearrangement.

  6. Variability of the Inner Proton Radiation Belt Observed by Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Li, X.; Selesnick, R.; Baker, D. N.; Jaynes, A. N.; Kanekal, S. G.; Hudson, M. K.; Kress, B. T.

    2015-12-01

    Inner radiation belt protons with kinetic energy above 10 MeV are known to be highly stable, with a maximum intensity near L = 1.5 that varies little evenon solar-cycle time scales. However, for L = 2 and above, more rapid changes occur: (1) protons are trapped during solar particle events, (2) steady intensity changes near L = 2 may result from radial diffusion, (3) for L > 2 there are rapid losses during magnetic storms, and (4) the losses are replenished by albedo neutron decay. New measurements from Van Allen Probes describe each of the last three processes in detail (the first has not yet been observed). These data provide new constraints on theories of trapped proton dynamics and improved empirical estimates of transport coefficients for radiation belt modeling.

  7. The Unique Capabilities of the Allen Telescope Array for Pulsar Timing and Gravitational Wave Detection

    NASA Astrophysics Data System (ADS)

    McLaughlin, Maura

    2011-01-01

    Since their discovery in 1982, millisecond pulsars have served as exquisite probes of fundamental physics. I will discuss the most transformative current application of millisecond pulsars: the direct detection of gravitational waves. Timing an array of pulsars could result in the detection of a stochastic background of gravitational waves, most likely resulting from an ensemble of supermassive black hole binaries. The unique capabilities of the Allen Telescope Array (ATA) will make it a very important resource for this experiment. The multi-wavelength coverage will increase sensitivity and enable optimal removal of interstellar propagation affects and the flexibility of scheduling afforded by commensal observing will increase the number of sources times and the cadence at which we can observe each source. I will discuss how these properties complement existing facilities and how including the ATA will increase the sensitivity of the international pulsar timing array.

  8. George Herbert Mead and the Allen controversy at the University of Wisconsin.

    PubMed

    Cook, Gary A

    2007-01-01

    This essay uses previously unpublished correspondence of George Herbert Mead to tell the story of his involvement in the aftermath of a political dispute that took place at the University of Wisconsin during the years 1914-1915. It seeks thereby to clarify the historical significance of an article he published on this controversy in late 1915. Taken together with relevant information about the educational activities of William H. Allen of the New York Bureau of Municipal Research, Mead's correspondence and article throw helpful light upon his understanding of how an educational survey of a university should proceed; they also show how he went about the task of evaluating a failed attempt at such a survey.

  9. Electron dropout echoes induced by interplanetary shock: Van Allen Probes observations

    NASA Astrophysics Data System (ADS)

    Hao, Y. X.; Zong, Q.-G.; Zhou, X.-Z.; Fu, S. Y.; Rankin, R.; Yuan, C.-J.; Lui, A. T. Y.; Spence, H. E.; Blake, J. B.; Baker, D. N.; Reeves, G. D.

    2016-06-01

    On 23 November 2012, a sudden dropout of the relativistic electron flux was observed after an interplanetary shock arrival. The dropout peaks at ˜1 MeV and more than 80% of the electrons disappeared from the drift shell. Van Allen twin Probes observed a sharp electron flux dropout with clear energy dispersion signals. The repeating flux dropout and recovery signatures, or "dropout echoes", constitute a new phenomenon referred to as a "drifting electron dropout" with a limited initial spatial range. The azimuthal range of the dropout is estimated to be on the duskside, from ˜1300 to 0100 LT. We conclude that the shock-induced electron dropout is not caused by the magnetopause shadowing. The dropout and consequent echoes suggest that the radial migration of relativistic electrons is induced by the strong dusk-dawn asymmetric interplanetary shock compression on the magnetosphere.

  10. The Toda System and Clustering Interfaces in the Allen Cahn equation

    NASA Astrophysics Data System (ADS)

    Del Pino, Manuel; Kowalczyk, Michał; Wei, Juncheng

    2008-10-01

    We consider the Allen Cahn equation {\\varepsilon2Δ u + (1-u^2)u = 0} in a bounded, smooth domain Ω in {mathbb{R}^2} , under zero Neumann boundary conditions, where {\\varepsilon > 0} is a small parameter. Let Γ0 be a segment contained in Ω, connecting orthogonally the boundary. Under certain nondegeneracy and nonminimality assumptions for Γ0, satisfied for instance by the short axis in an ellipse, we construct, for any given N ≥ 1, a solution exhibiting N transition layers whose mutual distances are {O(\\varepsilon|log\\varepsilon|)} and which collapse onto Γ0 as {\\varepsilonto 0} . Asymptotic location of these interfaces is governed by a Toda-type system and yields in the limit broken lines with an angle at a common height and at main order cutting orthogonally the boundary.

  11. Cobalt-Catalyzed sp(2) -C-H Activation: Intermolecular Heterocyclization with Allenes at Room Temperature.

    PubMed

    Thrimurtulu, Neetipalli; Dey, Arnab; Maiti, Debabrata; Volla, Chandra M R

    2016-09-26

    The reactivity of allenes in transition-metal-catalyzed C-H activation chemistry is governed by the formation of either alkenyl-metal (M-alkenyl) or metal-π-allyl intermediates. Although either protonation or a β-hydride elimination is feasible with a M-alkenyl intermediate, cyclization has remained unexplored to date. Furthermore, due to the increased steric hindrance, the regioselectivity for the intramolecular cyclization of the metal-π-allyl intermediate was hampered towards the more substituted side. To address these issues, a unified approach to synthesize a diverse array of biologically and pharmaceutically relevant heterocyclic moieties by cobalt-catalyzed directed C-H functionalization was envisioned. Upon successful implementation, the present strategy led to the regioselective formation of dihydroisoquinolin-1(2H)-ones, isoquinolin-1(2H)-ones, dihydropyridones, and pyridones. PMID:27584828

  12. Wave-driven butterfly distribution of Van Allen belt relativistic electrons.

    PubMed

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D N; Spence, H E; Funsten, H O; Blake, J B

    2015-01-01

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day-night asymmetry in Earth's magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. Simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. The current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons. PMID:26436770

  13. Pi2 Pulsations Observed by Van Allen Probes: A Case Study

    NASA Astrophysics Data System (ADS)

    Ghamry, E.; Kim, K. H.; Kwon, H. J.; Lee, D. H.; Kletzing, C.; Kurth, W. S.

    2014-12-01

    The plasmaspheric virtual resonance model has been proposed as one of the source mechanisms for low-latitude Pi2 pulsations. Few studies have used simultaneous multipoint observations in space to examine the spatial structure of Pi2 pulsations both inside and outside the plasmasphere. In this study we show multipoint observations for Pi2 pulsations using the Van Allen Probes (RBSP-A and RBSP-B). We focus on the two events that occurred between 1700 and 2000 UT on March 12, 2013, which were simultaneously observed by Van Allen Probes and Bohyun (BOH, L = 1.35) station in South Korea. By using plasma density measurements, we determined that during this time RBSP-A was located outside the plasmasphere and RBSP-B was located inside it. We found that the poloidal, radial (δBx) and compressional (δBz), magnetic field components, and the azimuthal (Ey) electric field component observed by both RBSP-A and RBSP-B have a high correlation with the H component at BOH for both events. The δBx and δBz oscillations at both RBSP-A and RBSP-B are nearly out of phase with ground Pi2. The Ey -H cross phases at RBSP-A outside the plasmapause and RBSP-B inside the plasmapause are nearly in quadrature for the first Pi2 event. These observations indicate that the Pi2 pulsations exist outside the plasmasphere with a radially standing signature which supports the plasmaspheric virtual resonance model.

  14. Formation of the oxygen torus in the inner magnetosphere: Van Allen Probes observations

    DOE PAGES

    Nose, Masahito; Oimatsu, S.; Keika, K.; Kletzing, C. A.; Kurth, W. S.; De Pascuale, S.; Smith, C. W.; MacDowall, R. J.; Reeves, Geoffrey D.; Nakano, S.; et al

    2015-02-19

    Here we study the formation process of an oxygen torus during the 12–15 November 2012 magnetic storm, using the magnetic field and plasma wave data obtained by Van Allen Probes. We estimate the local plasma mass density (ρL) and the local electron number density (neL) from the resonant frequencies of standing Alfvén waves and the upper hybrid resonance band. The average ion mass (M) can be calculated by M ~ ρL/neL under the assumption of quasi-neutrality of plasma. During the storm recovery phase, both Probe A and Probe B observe the oxygen torus at L = 3.0–4.0 and L =more » 3.7–4.5, respectively, on the morning side. The oxygen torus has M = 4.5–8 amu and extends around the plasmapause that is identified at L~3.2–3.9. We find that during the initial phase, M is 4–7 amu throughout the plasma trough and remains at ~1 amu in the plasmasphere, implying that ionospheric O+ ions are supplied into the inner magnetosphere already in the initial phase of the magnetic storm. Numerical calculation under a decrease of the convection electric field reveals that some of thermal O+ ions distributed throughout the plasma trough are trapped within the expanded plasmasphere, whereas some of them drift around the plasmapause on the dawnside. This creates the oxygen torus spreading near the plasmapause, which is consistent with the Van Allen Probes observations. We conclude that the oxygen torus identified in this study favors the formation scenario of supplying O+ in the inner magnetosphere during the initial phase and subsequent drift during the recovery phase.« less

  15. Formation of the oxygen torus in the inner magnetosphere: Van Allen Probes observations

    SciTech Connect

    Nose, Masahito; Oimatsu, S.; Keika, K.; Kletzing, C. A.; Kurth, W. S.; De Pascuale, S.; Smith, C. W.; MacDowall, R. J.; Reeves, Geoffrey D.; Nakano, S.; Spence, H. E.; Larsen, Brian Arthur

    2015-02-19

    Here we study the formation process of an oxygen torus during the 12–15 November 2012 magnetic storm, using the magnetic field and plasma wave data obtained by Van Allen Probes. We estimate the local plasma mass density (ρL) and the local electron number density (neL) from the resonant frequencies of standing Alfvén waves and the upper hybrid resonance band. The average ion mass (M) can be calculated by M ~ ρL/neL under the assumption of quasi-neutrality of plasma. During the storm recovery phase, both Probe A and Probe B observe the oxygen torus at L = 3.0–4.0 and L = 3.7–4.5, respectively, on the morning side. The oxygen torus has M = 4.5–8 amu and extends around the plasmapause that is identified at L~3.2–3.9. We find that during the initial phase, M is 4–7 amu throughout the plasma trough and remains at ~1 amu in the plasmasphere, implying that ionospheric O+ ions are supplied into the inner magnetosphere already in the initial phase of the magnetic storm. Numerical calculation under a decrease of the convection electric field reveals that some of thermal O+ ions distributed throughout the plasma trough are trapped within the expanded plasmasphere, whereas some of them drift around the plasmapause on the dawnside. This creates the oxygen torus spreading near the plasmapause, which is consistent with the Van Allen Probes observations. We conclude that the oxygen torus identified in this study favors the formation scenario of supplying O+ in the inner magnetosphere during the initial phase and subsequent drift during the recovery phase.

  16. Recent Performance Testing Results Using the 3-element Production Test Array for the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Tarter, J. C.; Blitz, L.; ATA 25 person Team; Paul G. Allen Foundation Collaboration

    2002-12-01

    The Allen Telescope Array will consist of 350 fixed six-meter dishes at the Hat Creek Radio Observatory in northern California (land use permits pending). It is the first massively parallel array ever built. Where possible, components from consumer markets and mass-production manufacturing processes have been used to lower costs. The architecture of the array explicitly anticipates future growth as a result of "Moore's Law" improvements. There will be many novel features of this array including ultra-wideband instantaneous frequency coverage from 0.5 to 11 GHz, a very wide field of view (2.5 degrees across at 21 cm), miniaturized 80K cryogenics, full bandwidth analog data transmission from the antennas to the Myhrvold central processing facility, dynamic null-formation and tracking of satellite interferers, and continuous multi-user support for radio astronomical research and SETI explorations. Starting in July 2000, the technology development for this array has been a collaboration between the Paul G. Allen Foundation and the ATA team located at the SETI Institute and at the Radio Astronomy Laboratory at UC Berkeley. A rapid prototyping array (RPA) consisting of seven COTS antennas and room temperature L-band receivers was erected in Orinda, CA in March 2001. Thanks to strong and continuing support from Sun Microsystems, the RPA has provided an invaluable testbed for software development and evaluation of RFI mitigation schemes. An operational 3-element Production Test Array (PTA) has been implemented at Hat Creek Observatory over the last few months. The antennas, drives, monitor and control software, and frontend components are near-final versions to be manufactured for the full array. This poster provides performance data from the first few months of testing with the PTA. A final decision on commitment for construction is expected by April 1, 2003.

  17. Generation and effects of EMIC waves observed by the Van Allen Probes on 18 March 2013

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Saikin, A.; Gamayunov, K. V.; Spence, H. E.; Larsen, B.; Geoffrey, R.; Smith, C. W.; Torbert, R. B.; Kurth, W. S.; Kletzing, C.

    2015-12-01

    Electromagnetic ion cyclotron (EMIC) waves play a crucial role in particle dynamics in the Earth's magnetosphere. The free energy for EMIC wave generation is usually provided by the temperature anisotropy of the energetic ring current ions. EMIC waves can in turn cause particle energization and losses through resonant wave-particle interactions. Using measurements from the Van Allen Probes, we perform a case study of EMIC waves and associated plasma conditions observed on 18 March 2013. From 0204 to 0211 UT, the Van Allen Probe-B detected He+-band EMIC wave activity in the post-midnight sector (MLT=4.6-4.9) at very low L-shells (L=2.6-2.9). The event occurred right outside the inward-pushed plasmapause in the early recovery phase of an intense geomagnetic storm - min. Dst = -132 nT at 2100 UT on 17 March 2013. During this event, the fluxes of energetic (> 1 keV), anisotropic O+ dominate both the H+ and He+ fluxes in this energy range. Meanwhile, O+ fluxes at low energies (< 0.1 keV) are low compared to H+ and He+ fluxes in the same energy range. The fluxes of <0.1 keV He+ are clearly enhanced during the wave event, indicating a signature of wave heating. To further confirm the association of the observed plasma features with the EMIC waves, we calculate the electron minimum resonant energy (Emin) and pitch angle diffusion coefficient (Dαα) of the EMIC wave packets by using nominal ion composition, derived total ion density from the frequencies of upper hybrid resonance, and measured ambient and wave magnetic field. EMIC wave growth rates are also calculated to evaluate the role of loss-cone distributed ring current ions in the EMIC wave generation.

  18. New results from the Colorado CubeSat and comparison with Van Allen Probes data

    NASA Astrophysics Data System (ADS)

    Li, X.

    2013-05-01

    The Colorado Student Space Weather Experiment (CSSWE) is a 3-unit (10cm x 10cm x 30cm) CubeSat mission funded by the NSF, launched into a highly inclined (650) low-Earth (490km x 790km) orbit on 09/13/12 as a secondary payload under NASA's Educational Launch of Nanosatellites (ELaNa) program. CSSWE contains a single science payload, the Relativistic Electron and Proton Telescope integrated little experiment (REPTile), which is a simplified and miniaturized version of the Relativistic Electron and Proton Telescope (REPT) built at the Laboratory for Atmospheric and Space Physics (LASP) of University of Colorado for NASA/Van Allen Probes mission, which consists of two identical spacecraft, launched on 08/30/12, that traverse the heart of the radiation belts in a low inclination (100) orbit. REPTile is designed to measure the directional differential flux of protons ranging from 9 to 40 MeV and electrons from 0.5 to >3.3 MeV. Three-month science mission (full success) was completed on 1/05/13. We are now into the extended mission phase, focusing on data analysis and modeling. REPTile measures a fraction of the total population that has small enough equatorial pitch angles to reach the altitude of CSSWE, thus measuring the precipitating population as well as the trapped population. These measurements are critical for understanding the loss of outer radiation belt electrons. New results from CSSWE and comparison with Van Allen Probes data will be presented. The CSSWE is also an ideal class project, involving over 65 graduate and undergraduate students and providing training for the next generation of engineers and scientists over the full life-cycle of a satellite project.

  19. Linolenate 9R-dioxygenase and allene oxide synthase activities of Lasiodiplodia theobromae.

    PubMed

    Jernerén, Fredrik; Eng, Felipe; Hamberg, Mats; Oliw, Ernst H

    2012-01-01

    Jasmonic acid (JA) is synthesized from linolenic acid (18:3n-3) by sequential action of 13-lipoxygenase, allene oxide synthase (AOS), and allene oxide cyclase. The fungus Lasiodiplodia theobromae can produce large amounts of JA and was recently reported to form the JA precursor 12-oxophytodienoic acid. The objective of our study was to characterize the fatty acid dioxygenase activities of this fungus. Two strains of L. theobromae with low JA secretion (~0.2 mg/L medium) oxygenated 18:3n-3 to 5,8-dihydroxy-9Z,12Z,15Z-octadecatrienoic acid as well as 9R-hydroperoxy-10E,12Z,15Z-octadecatrienoic acid, which was metabolized by an AOS activity into 9-hydroxy-10-oxo-12Z,15Z-octadecadienoic acid. Analogous conversions were observed with linoleic acid (18:2n-6). Studies using [11S-(2)H]18:2n-6 revealed that the putative 9R-dioxygenase catalyzed stereospecific removal of the 11R hydrogen followed by suprafacial attack of dioxygen at C-9. Mycelia from these strains of L. theobromae contained 18:2n-6 as the major polyunsaturated acid but lacked 18:3n-3. A third strain with a high secretion of JA (~200 mg/L) contained 18:3n-3 as a major fatty acid and produced 5,8-dihydroxy-9Z,12Z,15Z-octadecatrienoic acid from added 18:3n-3. This strain also lacked the JA biosynthetic enzymes present in higher plants. PMID:22048860

  20. MRI-based treatment planning with pseudo CT generated through atlas registration

    SciTech Connect

    Uh, Jinsoo Merchant, Thomas E.; Hua, Chiaho; Li, Yimei; Li, Xingyu

    2014-05-15

    Purpose: To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. Methods: A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. Results: The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787–0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%–98.7%) satisfied the criteria of chi-evaluation (<2% maximum dose and 2 mm range). The dose to 95% of the volume and the

  1. Distributed analysis in ATLAS

    NASA Astrophysics Data System (ADS)

    Dewhurst, A.; Legger, F.

    2015-12-01

    The ATLAS experiment accumulated more than 140 PB of data during the first run of the Large Hadron Collider (LHC) at CERN. The analysis of such an amount of data is a challenging task for the distributed physics community. The Distributed Analysis (DA) system of the ATLAS experiment is an established and stable component of the ATLAS distributed computing operations. About half a million user jobs are running daily on DA resources, submitted by more than 1500 ATLAS physicists. The reliability of the DA system during the first run of the LHC and the following shutdown period has been high thanks to the continuous automatic validation of the distributed analysis sites and the user support provided by a dedicated team of expert shifters. During the LHC shutdown, the ATLAS computing model has undergone several changes to improve the analysis workflows, including the re-design of the production system, a new analysis data format and event model, and the development of common reduction and analysis frameworks. We report on the impact such changes have on the DA infrastructure, describe the new DA components, and include recent performance measurements.

  2. MARS: a mouse atlas registration system based on a planar x-ray projector and an optical camera

    NASA Astrophysics Data System (ADS)

    Wang, Hongkai; Stout, David B.; Taschereau, Richard; Gu, Zheng; Vu, Nam T.; Prout, David L.; Chatziioannou, Arion F.

    2012-10-01

    This paper introduces a mouse atlas registration system (MARS), composed of a stationary top-view x-ray projector and a side-view optical camera, coupled to a mouse atlas registration algorithm. This system uses the x-ray and optical images to guide a fully automatic co-registration of a mouse atlas with each subject, in order to provide anatomical reference for small animal molecular imaging systems such as positron emission tomography (PET). To facilitate the registration, a statistical atlas that accounts for inter-subject anatomical variations was constructed based on 83 organ-labeled mouse micro-computed tomography (CT) images. The statistical shape model and conditional Gaussian model techniques were used to register the atlas with the x-ray image and optical photo. The accuracy of the atlas registration was evaluated by comparing the registered atlas with the organ-labeled micro-CT images of the test subjects. The results showed excellent registration accuracy of the whole-body region, and good accuracy for the brain, liver, heart, lungs and kidneys. In its implementation, the MARS was integrated with a preclinical PET scanner to deliver combined PET/MARS imaging, and to facilitate atlas-assisted analysis of the preclinical PET images.

  3. White matter atlas of the human spinal cord with estimation of partial volume effect.

    PubMed

    Lévy, S; Benhamou, M; Naaman, C; Rainville, P; Callot, V; Cohen-Adad, J

    2015-10-01

    Template-based analysis has proven to be an efficient, objective and reproducible way of extracting relevant information from multi-parametric MRI data. Using common atlases, it is possible to quantify MRI metrics within specific regions without the need for manual segmentation. This method is therefore free from user-bias and amenable to group studies. While template-based analysis is common procedure for the brain, there is currently no atlas of the white matter (WM) spinal pathways. The goals of this study were: (i) to create an atlas of the white matter tracts compatible with the MNI-Poly-AMU template and (ii) to propose methods to quantify metrics within the atlas that account for partial volume effect. The WM atlas was generated by: (i) digitalizing an existing WM atlas from a well-known source (Gray's Anatomy), (ii) registering this atlas to the MNI-Poly-AMU template at the corresponding slice (C4 vertebral level), (iii) propagating the atlas throughout all slices of the template (C1 to T6) using regularized diffeomorphic transformations and (iv) computing partial volume values for each voxel and each tract. Several approaches were implemented and validated to quantify metrics within the atlas, including weighted-average and Gaussian mixture models. Proof-of-concept application was done in five subjects for quantifying magnetization transfer ratio (MTR) in each tract of the atlas. The resulting WM atlas showed consistent topological organization and smooth transitions along the rostro-caudal axis. The median MTR across tracts was 26.2. Significant differences were detected across tracts, vertebral levels and subjects, but not across laterality (right-left). Among the different tested approaches to extract metrics, the maximum a posteriori showed highest performance with respect to noise, inter-tract variability, tract size and partial volume effect. This new WM atlas of the human spinal cord overcomes the biases associated with manual delineation and partial

  4. Software-based Diffusion MR Human Brain Phantom for Evaluating Fiber-tracking Algorithms.

    PubMed

    Shi, Yundi; Roger, Gwendoline; Vachet, Clement; Budin, Francois; Maltbie, Eric; Verde, Audrey; Hoogstoel, Marion; Berger, Jean-Baptiste; Styner, Martin

    2013-03-13

    Fiber tracking provides insights into the brain white matter network and has become more and more popular in diffusion MR imaging. Hardware or software phantom provides an essential platform to investigate, validate and compare various tractography algorithms towards a "gold standard". Software phantoms excel due to their flexibility in varying imaging parameters, such as tissue composition, SNR, as well as potential to model various anatomies and pathologies. This paper describes a novel method in generating diffusion MR images with various imaging parameters from realistically appearing, individually varying brain anatomy based on predefined fiber tracts within a high-resolution human brain atlas. Specifically, joint, high resolution DWI and structural MRI brain atlases were constructed with images acquired from 6 healthy subjects (age 22-26) for the DWI data and 56 healthy subject (age 18-59) for the structural MRI data. Full brain fiber tracking was performed with filtered, two-tensor tractography in atlas space. A deformation field based principal component model from the structural MRI as well as unbiased atlas building was then employed to generate synthetic structural brain MR images that are individually varying. Atlas fiber tracts were accordingly warped into each synthetic brain anatomy. Diffusion MR images were finally computed from these warped tracts via a composite hindered and restricted model of diffusion with various imaging parameters for gradient directions, image resolution and SNR. Furthermore, an open-source program was developed to evaluate the fiber tracking results both qualitatively and quantitatively based on various similarity measures. PMID:24357914

  5. Brain herniation

    MedlinePlus

    ... herniation; Uncal herniation; Subfalcine herniation; Tonsillar herniation; Herniation - brain ... Brain herniation occurs when something inside the skull produces pressure that moves brain tissues. This is most ...

  6. Maximum-margin based representation learning from multiple atlases for Alzheimer's disease classification.

    PubMed

    Min, Rui; Cheng, Jian; Price, True; Wu, Guorong; Shen, Dinggang

    2014-01-01

    In order to establish the correspondences between different brains for comparison, spatial normalization based morphometric measurements have been widely used in the analysis of Alzheimer's disease (AD). In the literature, different subjects are often compared in one atlas space, which may be insufficient in revealing complex brain changes. In this paper, instead of deploying one atlas for feature extraction and classification, we propose a maximum-margin based representation learning (MMRL) method to learn the optimal representation from multiple atlases. Unlike traditional methods that perform the representation learning separately from the classification, we propose to learn the new representation jointly with the classification model, which is more powerful in discriminating AD patients from normal controls (NC). We evaluated the proposed method on the ADNI database, and achieved 90.69% for AD/NC classification and 73.69% for p-MCI/s-MCI classification.

  7. [Medical image segmentation based on guided filtering and multi-atlas].

    PubMed

    Wen, Rui; Chen, Hongwen; Zhang, Lei; Lu, Zhentai

    2015-08-01

    A novel medical automatic image segmentation strategy based on guided filtering and multi-atlas is proposed to achieve accurate, smooth, robust, and reliable segmentation. This framework consists of 4 elements: the multi-atlas registration, which uses the atlas prior information; the label fusion, in which the similarity measure of the registration is used as the weight to fuse the warped label; the guided filtering, which uses the local information of the target image to correct the registration errors; and the threshold approaches used to obtain the segment result. The experimental results showed part among the 15 brain MRI images used to segment the hippocampus region, the proposed method achieved a median Dice coefficient of 86% on the left hippocampus and 87.4% on the right hippocampus. Compared with the traditional label fusion algorithm, the proposed algorithm outperforms the common brain image segmentation methods with a good efficiency and accuracy. PMID:26403735

  8. Atlas of neuroanatomy with radiologic correlation and pathologic illustration

    SciTech Connect

    Dublin, A.B.; Dublin, W.B.

    1982-01-01

    This atlas correlates gross neuroanatomic specimens with radiographs and computed tomographic scans. Pathologic specimens and radiographs are displayed in a similar manner. The first chapter, on embryology, shows the development of the telencephalon, diencephalon, mesencephalon, and metencephalon through a series of overlays. The anatomical section shows the surface of the brain, the ventricles and their adjacent structures, and the vascular system. CT anatomy is demonstrated by correlating CT scans with pathologic brain specimens cut in the axial plane. Pathologic changes associated with congenital malformations, injections, injuries, tumors, and other causes are demonstrated in the last six chapters.

  9. Analysis Preservation in ATLAS

    NASA Astrophysics Data System (ADS)

    Cranmer, Kyle; Heinrich, Lukas; Jones, Roger; South, David M.

    2015-12-01

    Long before data taking, ATLAS established a policy that all analyses need to be preserved. In the initial data-taking period, this has been achieved by various tools and techniques. ATLAS is now reviewing the analysis preservation with the aim of bringing coherence and robustness to the process and with a clearer view of the level of reproducibility that is reasonably achievable. The secondary aim is to reduce the load on the analysts. Once complete, this will serve for our internal preservation needs but also provide a basis for any subsequent sharing of analysis results with external parties.

  10. The Herschel ATLAS

    NASA Technical Reports Server (NTRS)

    Eales, S.; Dunne, L.; Clements, D.; Cooray, A.; De Zotti, G.; Dye, S.; Ivison, R.; Jarvis, M.; Lagache, G.; Maddox, S.; Negrello, M.; Serjeant, S.; Thompson, M. A.; Van Kampen, E.; Amblard, A.; Andreani, P.; Baes, M.; Beelen, A.; Bendo, G. J.; Bertoldi, F.; Benford, D.; Bock, J.

    2010-01-01

    The Herschel ATLAS is the largest open-time key project that will be carried out on the Herschel Space Observatory. It will survey 570 sq deg of the extragalactic sky, 4 times larger than all the other Herschel extragalactic surveys combined, in five far-infrared and submillimeter bands. We describe the survey, the complementary multiwavelength data sets that will be combined with the Herschel data, and the six major science programs we are undertaking. Using new models based on a previous submillimeter survey of galaxies, we present predictions of the properties of the ATLAS sources in other wave bands.

  11. Rhodium-catalyzed (5+1) annulations between 2-alkenylphenols and allenes: a practical entry to 2,2-disubstituted 2H-chromenes.

    PubMed

    Casanova, Noelia; Seoane, Andrés; Mascareñas, José L; Gulías, Moisés

    2015-02-16

    Readily available alkenylphenols react with allenes under rhodium catalysis to provide valuable 2,2-disubstituted 2H-chromenes. The whole process, which involves the cleavage of one C-H bond of the alkenyl moiety and the participation of the allene as a one-carbon cycloaddition partner, can be considered a simple, versatile, and atom-economical (5+1) heteroannulation. The reaction tolerates a broad range of substituents both in the alkenylphenol and in the allene, and most probably proceeds through a mechanism involving a rhodium-catalyzed C-C coupling followed by two sequential pericyclic processes.

  12. Predicting aphasia type from brain damage measured with structural MRI.

    PubMed

    Yourganov, Grigori; Smith, Kimberly G; Fridriksson, Julius; Rorden, Chris

    2015-12-01

    Chronic aphasia is a common consequence of a left-hemisphere stroke. Since the early insights by Broca and Wernicke, studying the relationship between the loci of cortical damage and patterns of language impairment has been one of the concerns of aphasiology. We utilized multivariate classification in a cross-validation framework to predict the type of chronic aphasia from the spatial pattern of brain damage. Our sample consisted of 98 patients with five types of aphasia (Broca's, Wernicke's, global, conduction, and anomic), classified based on scores on the Western Aphasia Battery (WAB). Binary lesion maps were obtained from structural MRI scans (obtained at least 6 months poststroke, and within 2 days of behavioural assessment); after spatial normalization, the lesions were parcellated into a disjoint set of brain areas. The proportion of damage to the brain areas was used to classify patients' aphasia type. To create this parcellation, we relied on five brain atlases; our classifier (support vector machine - SVM) could differentiate between different kinds of aphasia using any of the five parcellations. In our sample, the best classification accuracy was obtained when using a novel parcellation that combined two previously published brain atlases, with the first atlas providing the segmentation of grey matter, and the second atlas used to segment the white matter. For each aphasia type, we computed the relative importance of different brain areas for distinguishing it from other aphasia types; our findings were consistent with previously published reports of lesion locations implicated in different types of aphasia. Overall, our results revealed that automated multivariate classification could distinguish between aphasia types based on damage to atlas-defined brain areas. PMID:26465238

  13. volBrain: An Online MRI Brain Volumetry System.

    PubMed

    Manjón, José V; Coupé, Pierrick

    2016-01-01

    The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results. PMID:27512372

  14. volBrain: An Online MRI Brain Volumetry System.

    PubMed

    Manjón, José V; Coupé, Pierrick

    2016-01-01

    The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results.

  15. volBrain: An Online MRI Brain Volumetry System

    PubMed Central

    Manjón, José V.; Coupé, Pierrick

    2016-01-01

    The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results. PMID:27512372

  16. Van Allen Probes Mission Space Academy: Educating middle school students about Earth's mysterious radiation belts

    NASA Astrophysics Data System (ADS)

    Butler, L.; Turney, D.; Matiella Novak, A.; Smith, D.; Simon, M.

    2013-12-01

    How's the weather in space? Why on Earth did NASA send two satellites above Earth to study radiation belts and space weather? To learn the answer to questions about NASA's Van Allen Probes mission, 450 students and their teachers from Maryland middle schools attended Space Academy events highlighting the Van Allen Probes mission. Sponsored by the Applied Physics Laboratory (APL) and Discovery Education, the events are held at the APL campus in Laurel, MD. Space Academies take students and teachers on behind-the-scenes exploration of how spacecraft are built, what they are designed to study, and introduces them to the many professionals that work together to create some of NASA's most exciting projects. Moderated by a public relations representative in the format of an official NASA press conference, the daylong event includes a student press conference with students as reporters and mission experts as panelists. Lunch with mission team members gives students a chance to ask more questions. After lunch, students don souvenir clean room suits, enjoy interactive science demonstrations, and tour APL facilities where the Van Allen Probes were built and tested before launch. Students may even have an opportunity to peek inside a clean room to view spacecraft being assembled. Prior to the event, teachers are provided with classroom activities, lesson plans, and videos developed by APL and Discovery Education to help prepare students for the featured mission. The activities are aligned to National Science Education Standards and appropriate for use in the classroom. Following their visit, student journalists are encouraged to write a short article about their field trip; selections are posted on the Space Academy web site. Designed to engage, inspire, and influence attitudes about space science and STEM careers, Space Academies provide an opportunity to attract underserved populations and emphasize that space science is for everyone. Exposing students to a diverse group of

  17. Simultaneous Pi2 observations by the Van Allen Probes inside and outside the plasmasphere

    NASA Astrophysics Data System (ADS)

    Ghamry, E.; Kim, K.-H.; Kwon, H.-J.; Lee, D.-H.; Park, J.-S.; Choi, J.; Hyun, K.; Kurth, W. S.; Kletzing, C.; Wygant, J. R.; Huang, J.

    2015-06-01

    Plasmaspheric virtual resonance (PVR) model has been proposed as one of source mechanisms for low-latitude Pi2 pulsations. Since PVR-associated Pi2 pulsations are not localized inside the plasmasphere, simultaneous multipoint observations inside and outside the plasmasphere require to test the PVR model. Until now, however, there are few studies using simultaneous multisatellite observations inside and outside the plasmasphere for understanding the radial structure of Pi2 pulsation. In this study, we focus on the Pi2 event observed at low-latitude Bohyun (BOH, L = 1.35) ground station in South Korea in the postmidnight sector (magnetic local time (MLT) = 3.0) for the interval from 1730 to 1900 UT on 12 March 2013. By using electron density derived from the frequency of the upper hybrid waves detected at Van Allen Probe-A (VAP-A) and Van Allen Probe-B (VAP-B), the plasmapause is identified. At the time of the Pi2 event, VAP-A was outside the plasmasphere near midnight (00:55 MLT and L =˜ 6), while VAP-B was inside the plasmasphere in the postmidnight sector (02:15 MLT and L =˜ 5). VAP-B observed oscillations in the compressional magnetic field component (Bz) and the dawn-to-dusk electric field component (Ey), having high coherence with the BOH Pi2 pulsation in the H component. The H-Bz and H-Ey cross phases at VAP-B inside the plasmasphere were near -180° and -90°, respectively. These phase relationships among Bz, Ey, and H are consistent with a radially standing oscillation of the fundamental mode reported in previous studies. At VAP-A outside the plasmasphere, Bz oscillations were highly correlated with BOH Pi2 pulsations with ˜-180° phase delay, and the H-Ey cross phase is near -90°. From these two-satellite observations, we suggest that the fundamental PVR mode is directly detected by VAP-A and VAP-B.

  18. Cycloaddition reactions of allenylphosphonates and related allenes with dialkyl acetylenedicarboxylates, 1,3-diphenylisobenzofuran, and anthracene.

    PubMed

    Sajna, K V; Kotikalapudi, Ramesh; Chakravarty, Manab; Bhuvan Kumar, N N; Swamy, K C Kumara

    2011-02-01

    Cycloaddition reactions of allenylphosphonates [(RO)(2)P(O)[(R(1))C═C═CR(2)(2)] with dialkyl acetylenedicarboxylates, 1,3-diphenylisobenzofuran, and anthracene have been investigated and compared with those of allenoates [(EtO(2)C)RC═C═CH(2)] and allenylphosphine oxides [Ph(2)P(O)(R(1))C═C═CR(2)(2)] in selected cases. Allenylphosphonates (RO)(2)P(O)(Ar)C═C═CH(2) with an α-aryl group preferentially undergo [4 + 2] cycloaddition with DMAD/DEAD under thermal activation, but in addition to the expected 1:1 (allene: DMAD) product, the reaction also leads to 1:2 as well as 2:1 products that were not reported before. When an extra vinyl group is present at the γ-carbon of allenylphosphonate [e.g., (OCH(2)CMe(2)CH(2)O)P(O)(Ph)C═C═CH(C═CHMe)], [4 + 2] cycloaddition takes place utilizing either the vinylic or the aryl end, but additionally a novel cyclization wherein complete opening of the [β,γ] carbon-carbon double bond of the allene is realized. In contrast to these, the reaction of allenylphosphonate (OCH(2)CMe(2)CH(2)O)P(O)(H)C═C═CMe(2) possessing a terminal ═CMe(2) group with DMAD occurs by both [2 + 2] cycloaddition and ene reaction. While the reaction of ═CH(2) terminal allenylphosphonates as well as allenylphosphine oxides with 1,3-diphenylisobenzofuran afforded preferentially endo-[4 + 2] cycloaddition products via [α,β] attack, the analogous allenoates [(EtO(2)C)RC═C═CH(2)] underwent exo-[4 + 2] cyclization. Under similar conditions, allenylphosphonates with a terminal ═CR(2) group gave only [β,γ]-cycloaddition products. An unusual ring-opening of a [4 + 2] cycloaddition product followed by ring-closing via [4 + 4] cycloaddition, as revealed by (31)P NMR spectroscopy, is reported. Anthracene reacted in a manner similar to 1,3-diphenylisobenzofuran, albeit with lower reactivity. Key products, including a set of exo- and endo- [4 + 2] cycloaddition products, have been characterized by single crystal X-ray crystallography.

  19. Expression of Fusion Proteins of Aspergillus terreus Reveals a Novel Allene Oxide Synthase*

    PubMed Central

    Hoffmann, Inga; Jernerén, Fredrik; Oliw, Ernst H.

    2013-01-01

    Aspergilli oxidize C18 unsaturated fatty acids by dioxygenase-cytochrome P450 fusion proteins to signal molecules involved in reproduction and host-pathogen interactions. Aspergillus terreus expresses linoleate 9R-dioxygenase (9R-DOX) and allene oxide synthase (AOS) activities in membrane fractions. The genome contains five genes (ATEG), which may code for a 9R-DOX-AOS fusion protein. The genes were cloned and expressed, but none of them oxidized 18:2n-6 to 9R-hydroperoxy-10(E),12(Z)-octadecadienoic acid (9R-HPODE). ATEG_02036 transformed 9R-HPODE to an unstable allene oxide, 9(R),10-epoxy-10,12(Z)-octadecadienoic acid. A substitution in the P450 domain (C1073S) abolished AOS activity. The N964V and N964D mutants both showed markedly reduced AOS activity, suggesting that Asn964 may facilitate homolytic cleavage of the dioxygen bond of 9R-HPODE with formation of compound II in analogy with plant AOS (CYP74) and prostacyclin synthase (CYP8A1). ATEG_03992 was identified as 5,8-linoleate diol synthase (5,8-LDS). Replacement of Asn878 in 5,8-LDS with leucine (N878L) mainly shifted ferryl oxygen insertion from C-5 toward C-6, but replacements of Gln881 markedly affected catalysis. The Q881L mutant virtually abolished the diol synthase activity. Replacement of Gln881 with Asn, Glu, Asp, or Lys residues augmented the homolytic cleavage of 8R-HPODE with formation of 10-hydroxy-8(9)-epoxy-12(Z)-octadecenoic acid (erythro/threo, 1–4:1) and/or shifted ferryl oxygen insertion from C-5 toward C-11. We conclude that homolysis and heterolysis of the dioxygen bond with formation of compound II in AOS and compound I in 5,8-LDS are influenced by Asn and Gln residues, respectively, of the I-helices. AOS of A. terreus appears to have evolved independently of CYP74 but with an analogous reaction mechanism. PMID:23479731

  20. Big Sky Carbon Atlas

    DOE Data Explorer

    The Big Sky Carbon Atlas is an online geoportal designed for you to discover, interpret, and access geospatial data and maps relevant to decision support and education on carbon sequestration in the Big Sky Region. In serving as the public face of the Partnership's spatial Data Libraries, the Atlas provides a gateway to geographic information characterizing CO2 sources, potential geologic sinks, terrestrial carbon fluxes, civil and energy infrastructure, energy use, and related themes. In addition to directly serving the BSCSP and its stakeholders, the Atlas feeds regional data to the NatCarb Portal, contributing to a national perspective on carbon sequestration. Established components of the Atlas include a gallery of thematic maps and an interactive map that allows you to: • Navigate and explore regional characterization data through a user-friendly interface • Print your map views or publish them as PDFs • Identify technical references relevant to specific areas of interest • Calculate straight-line or pipeline-constrained distances from point sources of CO2 to potential geologic sink features • Download regional data layers (feature under development) (Acknowledgment to the Big Sky Carbon Sequestration Partnership (BSCSP); see home page at http://www.bigskyco2.org/)